rs4648356 chr:1 pos:

MMEL1(TNFRSF14)

rs11810217 chr:1 pos:

EVI5

rs11581062 chr:1 pos:

VCAM1

rs1335532 chr:1 pos:

CD58

rs1323292 chr:1 pos:

RGS1

rs7522462 chr:1 pos:

C1orf106(KIF21B)

rs12466022 chr:2 pos:

No gene

rs7595037 chr:2 pos:

PLEK

rs17174870 chr:2 pos:

MERTK

rs10201872 chr:2 pos:

SP140

rs11129295 chr:3 pos:

EOMES

rs669607 chr:3 pos:

No gene

rs2028597 chr:3 pos:

CBLB

rs2293370 chr:3 pos:

TMEM39A(CD80)

rs9282641 chr:3 pos:

CD86

rs2243123 chr:3 pos:

IL12A

rs228614 chr:4 pos:

NFKB1(MANBA)

rs6897932 chr:5 pos:

IL7R

rs4613763 chr:5 pos:

PTGER4

rs2546890 chr:5 pos:

IL12B

rs12212193 chr:6 pos:

BACH2

rs802734 chr:6 pos:

THEMIS

rs11154801 chr:6 pos:

MYB(AHI1)

rs17066096 chr:6 pos:

IL22RA2

rs13192841 chr:6 pos:

No gene

rs1738074 chr:6 pos:

TAGAP

rs354033 chr:7 pos:

ZNF746

rs1520333 chr:8 pos:

IL7

rs4410871 chr:8 pos:

MYC

rs2019960 chr:8 pos:

PVT1

rs3118470 chr:10 pos:

IL2RA

rs1250550 chr:10 pos:

ZMIZ1

rs7923837 chr:10 pos:

HHEX

rs650258 chr:11 pos:

CD6

rs630923 chr:11 pos:

CXCR5

rs1800693 chr:12 pos:

TNFRSF1A

rs10466829 chr:12 pos:

CLECL1

rs12368653 chr:12 pos:

CYP27B1

rs949143 chr:12 pos:

ARL6IP4

rs4902647 chr:14 pos:

ZFP36L1

rs2300603 chr:14 pos:

BATF

rs2119704 chr:14 pos:

GALC(GPR65)

rs2744148 chr:16 pos:

SOX8

rs7200786 chr:16 pos:

CLEC16A(CIITA)

rs13333054 chr:16 pos:

IRF8

rs9891119 chr:17 pos:

STAT3

rs180515 chr:17 pos:

RPS6KB1

rs7238078 chr:18 pos:

MALT1

rs1077667 chr:19 pos:

TNFSF14

rs8112449 chr:19 pos:

TYK2(ICAM3)

rs874628 chr:19 pos:

MPV17L2(IL12RB1)

rs2303759 chr:19 pos:

DKKL1(CD37)

rs2425752 chr:20 pos:

CD40

rs2248359 chr:20 pos:

CYP24A1

rs6062314 chr:20 pos:

TNFRSF6B

rs2283792 chr:22 pos:

MAPK1

rs140522 chr:22 pos:

SCO2

Multiple Sclerosis GWAS Browser

This site accompanies the article "Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis", The International Multiple Sclerosis Genetics Consortium (IMSGC) and the Wellcome Trust Case Control Consortium 2 (WTCCC2), Nature (2011). The data sources for this page are those described in the above article, and were current at the time of article preparation. Show more details

Overview. The plot on the left depicts regions of the human genome which have been found to be statistically associated with Multiple Sclerosis, as described in the above article. The vertical axis represents position along the human genome, with chromosome 1 at the top and chromosome 22 at the bottom, in alternating dark and light blue. (Sex chromosomes are not shown.) The horizontal axis represents the -log10 p-value for each locus (a measure of the evidence for association, see the article for details of the tests used), with points to the right having the most evidence and points to the left the least. Genetic loci highlighted in the article as associated with, or as showing strong evidence for association with Multiple Sclerosis are highlighted in red, with nearby genes identified by name. 57 loci are highlighted in total, with loci that were newly identified in the article indicated with bold gene names, loci with strong evidence for association (as defined in the article) in black and previously reported loci in grey. (The HLA region on chromosome 6 is not highlighted here because, although associated, the pattern of variation in the HLA is more complicated than at other loci.) Clicking on a locus or a gene name shows details of the association signal at the locus, including signal plots, rsid and allele frequencies for the lead SNP, and details relevant to the choice of candidate gene. Regional association plots for these and 47 additional loci that were taken to replication are available here (gzipped tarball, 9.1Mb). P-values for SNPs typed in the discovery phase can also be viewed in the relevant track of the T1DBase genome browser. Full data, including genotypes, are held by the European Genotype Archive and are available to researchers via the application process described on this page. See the article and its supplementary material for more information. Hide this overview

Click on a gene name to view more information.

Region

dbSNP id:rs4648356
status:previously reported
physical position:01:2,699,024
association region:01:2,396,586-2,827,369
functional tag:Non-synonymous coding (MMEL1)
nearest gene:MMEL1
candidate gene:MMEL1

Signal

p-value discovery:3.1e-14
OR discovery (95% CI):1.16 (1.12-1.21)
p-value replication:8.50e-03 (one-sided)
OR replication (95% CI):1.08 (1.01-1.15)
p-value combined:1.00e-14
OR combined (95% CI):1.14 (1.12-1.16)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

C1orf93, HES5, LOC115110, MMEL1, PANK4, PLCH2, TNFRSF14

Links

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Region

dbSNP id:rs11810217
status:previously reported
physical position:01:92,920,965
association region:01:92,014,277-93,306,499
functional tag:Non-synonymous coding (EVI5)
nearest gene:EVI5
candidate gene:EVI5

Signal

p-value discovery:6.5e-12
OR discovery (95% CI):1.15 (1.11-1.2)
p-value replication:1.00e-04 (one-sided)
OR replication (95% CI):1.14 (1.06-1.22)
p-value combined:5.80e-15
OR combined (95% CI):1.15 (1.13-1.16)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

BRDT, BTBD8, C1orf146, EPHX4, EVI5, FAM69A, GFI1, GLMN, KIAA1107, MTF2, RPAP2, RPL5, SNORA66, SNORD21, TGFBR3

Links

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Region

dbSNP id:rs11581062
status:novel association
physical position:01:101,180,107
association region:01:100,983,315-101,455,310
functional tag:N/A
nearest gene:SLC30A7
candidate gene:VCAM1

Signal

p-value discovery:3.7e-10
OR discovery (95% CI):1.13 (1.09-1.18)
p-value replication:4.20e-02 (one-sided)
OR replication (95% CI):1.07 (0.99-1.15)
p-value combined:2.50e-10
OR combined (95% CI):1.12 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

DPH5, EXTL2, S1PR1, SLC30A7, VCAM1

Links

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Region

dbSNP id:rs1335532
status:previously reported
physical position:01:116,902,480
association region:01:116,832,232-116,909,542
functional tag:N/A
nearest gene:CD58
candidate gene:CD58

Signal

p-value discovery:2e-09
OR discovery (95% CI):1.18 (1.12-1.24)
p-value replication:3.90e-10 (one-sided)
OR replication (95% CI):1.38 (1.24-1.52)
p-value combined:3.20e-16
OR combined (95% CI):1.22 (1.19-1.24)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

CD58, IGSF3

Links

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Region

dbSNP id:rs1323292
status:previously reported
physical position:01:190,807,644
association region:01:190,733,439-190,814,781
functional tag:N/A
nearest gene:RGS1
candidate gene:RGS1

Signal

p-value discovery:8.8e-07
OR discovery (95% CI):1.12 (1.07-1.18)
p-value replication:3.90e-03 (one-sided)
OR replication (95% CI):1.12 (1.03-1.21)
p-value combined:2.30e-08
OR combined (95% CI):1.12 (1.1-1.14)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

RGS1

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs7522462
status:previously reported
physical position:01:199,148,218
association region:01:199,128,354-199,336,605
functional tag:Non-synonymous coding (C1orf106)
nearest gene:C1orf106
candidate gene:C1orf106

Signal

p-value discovery:9.2e-07
OR discovery (95% CI):1.11 (1.06-1.15)
p-value replication:2.40e-04 (one-sided)
OR replication (95% CI):1.13 (1.05-1.21)
p-value combined:1.90e-09
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

C1orf106, CACNA1S, GPR25, KIF21B

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs12466022
status:novel association
physical position:02:43,212,565
association region:02:43,165,922-43,216,721
functional tag:N/A
nearest gene:(none)
candidate gene:(none)

Signal

p-value discovery:1.1e-06
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:3.00e-05 (one-sided)
OR replication (95% CI):1.16 (1.08-1.24)
p-value combined:6.20e-10
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs7595037
status:novel association
physical position:02:68,500,599
association region:02:68,387,193-68,534,474
functional tag:N/A
nearest gene:PLEK
candidate gene:PLEK

Signal

p-value discovery:6.5e-07
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:3.40e-06 (one-sided)
OR replication (95% CI):1.15 (1.08-1.22)
p-value combined:5.10e-11
OR combined (95% CI):1.11 (1.1-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

APLF, CNRIP1, FBXO48, PLEK

Links

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Region

dbSNP id:rs17174870
status:novel association
physical position:02:112,381,672
association region:02:112,361,731-112,961,046
functional tag:Essential splice site (MERTK)
nearest gene:MERTK
candidate gene:MERTK

Signal

p-value discovery:7.8e-06
OR discovery (95% CI):1.1 (1.06-1.15)
p-value replication:1.40e-04 (one-sided)
OR replication (95% CI):1.15 (1.06-1.23)
p-value combined:1.30e-08
OR combined (95% CI):1.11 (1.09-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

ANAPC1, FBLN7, MERTK, TMEM87B, TTL, ZC3H6, ZC3H8

Links

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Region

dbSNP id:rs10201872
status:novel association
physical position:02:230,814,968
association region:02:230,786,908-230,943,610
functional tag:N/A
nearest gene:SP140
candidate gene:SP140

Signal

p-value discovery:9.7e-08
OR discovery (95% CI):1.13 (1.08-1.19)
p-value replication:2.20e-04 (one-sided)
OR replication (95% CI):1.15 (1.06-1.24)
p-value combined:1.80e-10
OR combined (95% CI):1.14 (1.12-1.16)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

SP110, SP140, SP140L

Links

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Region

dbSNP id:rs11129295
status:novel association
physical position:03:27,763,784
association region:03:27,696,539-27,815,543
functional tag:N/A
nearest gene:EOMES
candidate gene:EOMES

Signal

conditional on:rs669607
p-value discovery:2.3e-08
OR discovery (95% CI):1.11 (1.07-1.16)
p-value replication:6.50e-03 (one-sided)
OR replication (95% CI):1.09 (1.02-1.16)
p-value combined:1.20e-09
OR combined (95% CI):1.11 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

EOMES

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs669607
status:novel association
physical position:03:28,046,448
association region:03:28,017,551-28,162,135
functional tag:N/A
nearest gene:(none)
candidate gene:(none)

Signal

p-value discovery:2.9e-11
OR discovery (95% CI):1.13 (1.09-1.17)
p-value replication:5.60e-06 (one-sided)
OR replication (95% CI):1.15 (1.08-1.23)
p-value combined:1.90e-15
OR combined (95% CI):1.13 (1.12-1.15)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs2028597
status:previously reported
physical position:03:107,041,527
association region:03:106,855,817-107,154,331
functional tag:N/A
nearest gene:CBLB
candidate gene:CBLB

Signal

p-value discovery:0.00021
OR discovery (95% CI):1.13 (1.06-1.21)
p-value replication:N/A?
OR replication (95% CI):N/A
p-value combined:N/A?
OR combined (95% CI):N/A
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CBLB

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs2293370
status:previously reported
physical position:03:120,702,624
association region:03:120,584,165-120,781,518
functional tag:Non-synonymous coding (TMEM39A)
nearest gene:C3orf1
candidate gene:TMEM39A

Signal

p-value discovery:1.1e-09
OR discovery (95% CI):1.16 (1.11-1.22)
p-value replication:6.90e-02 (one-sided)
OR replication (95% CI):1.06 (0.98-1.14)
p-value combined:2.70e-09
OR combined (95% CI):1.13 (1.11-1.15)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

ADPRH, C3orf1, CD80, CDGAP, KTELC1, PLA1A, TMEM39A

Links

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Region

dbSNP id:rs9282641
status:novel association
physical position:03:123,279,458
association region:03:123,097,536-123,454,717
functional tag:N/A
nearest gene:CD86
candidate gene:CD86

Signal

p-value discovery:1.5e-09
OR discovery (95% CI):1.21 (1.14-1.29)
p-value replication:8.70e-04 (one-sided)
OR replication (95% CI):1.2 (1.07-1.34)
p-value combined:1.00e-11
OR combined (95% CI):1.21 (1.18-1.24)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CASR, CD86, EAF2, ILDR1, SLC15A2

Links

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Region

dbSNP id:rs2243123
status:previously reported
physical position:03:161,192,345
association region:03:161,064,425-161,240,687
functional tag:N/A
nearest gene:IL12A
candidate gene:IL12A

Signal

p-value discovery:3.7e-06
OR discovery (95% CI):1.09 (1.05-1.14)
p-value replication:1.90e-01 (one-sided)
OR replication (95% CI):1.03 (0.96-1.11)
p-value combined:7.20e-06
OR combined (95% CI):1.08 (1.06-1.1)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

IL12A, SCHIP1

Links

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Region

dbSNP id:rs228614
status:strong evidence
physical position:04:103,797,685
association region:04:103,608,587-104,594,517
functional tag:N/A
nearest gene:MANBA
candidate gene:NFKB1

Signal

p-value discovery:9.1e-06
OR discovery (95% CI):1.09 (1.05-1.13)
p-value replication:2.40e-03 (one-sided)
OR replication (95% CI):1.09 (1.03-1.16)
p-value combined:1.40e-07
OR combined (95% CI):1.09 (1.07-1.1)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

BDH2, CENPE, CISD2, MANBA, NFKB1, NHEDC1, NHEDC2, UBE2D3

Links

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Region

dbSNP id:rs6897932
status:previously reported
physical position:05:35,910,332
association region:05:35,674,799-36,188,926
functional tag:Non-synonymous coding (IL7R)
nearest gene:IL7R
candidate gene:IL7R

Signal

p-value discovery:2.6e-06
OR discovery (95% CI):1.11 (1.06-1.16)
p-value replication:8.80e-04 (one-sided)
OR replication (95% CI):1.11 (1.04-1.19)
p-value combined:1.70e-08
OR combined (95% CI):1.11 (1.09-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CAPSL, IL7R, LMBRD2, SKP2, SPEF2, UGT3A1, UGT3A2

Links

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Region

dbSNP id:rs4613763
status:previously reported
physical position:05:40,428,485
association region:05:40,269,348-40,718,595
functional tag:N/A
nearest gene:PTGER4
candidate gene:PTGER4

Signal

p-value discovery:6.9e-14
OR discovery (95% CI):1.21 (1.15-1.28)
p-value replication:3.00e-04 (one-sided)
OR replication (95% CI):1.16 (1.07-1.27)
p-value combined:2.50e-16
OR combined (95% CI):1.2 (1.18-1.22)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

PTGER4

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs2546890
status:novel association
physical position:05:158,692,478
association region:05:158,433,068-158,758,750
functional tag:N/A
nearest gene:IL12B
candidate gene:IL12B

Signal

p-value discovery:2.7e-07
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:2.00e-06 (one-sided)
OR replication (95% CI):1.15 (1.09-1.22)
p-value combined:1.20e-11
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

EBF1, IL12B, RNF145, UBLCP1

Links

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Region

dbSNP id:rs12212193
status:novel association
physical position:06:91,053,490
association region:06:90,866,998-91,148,913
functional tag:N/A
nearest gene:BACH2
candidate gene:BACH2

Signal

p-value discovery:9.9e-07
OR discovery (95% CI):1.09 (1.05-1.13)
p-value replication:5.70e-03 (one-sided)
OR replication (95% CI):1.08 (1.02-1.15)
p-value combined:3.80e-08
OR combined (95% CI):1.09 (1.08-1.1)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

BACH2

Links

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Region

dbSNP id:rs802734
status:novel association
physical position:06:128,320,491
association region:06:127,860,104-128,384,638
functional tag:N/A
nearest gene:PTPRK
candidate gene:THEMIS

Signal

p-value discovery:1.6e-06
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:3.40e-04 (one-sided)
OR replication (95% CI):1.13 (1.05-1.21)
p-value combined:5.50e-09
OR combined (95% CI):1.1 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

C6orf174, C6orf58, KIAA0408, PTPRK, THEMIS

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs11154801
status:novel association
physical position:06:135,781,048
association region:06:135,630,175-136,250,729
functional tag:N/A
nearest gene:AHI1
candidate gene:MYB

Signal

p-value discovery:1.5e-12
OR discovery (95% CI):1.15 (1.1-1.19)
p-value replication:3.50e-03 (one-sided)
OR replication (95% CI):1.09 (1.02-1.16)
p-value combined:1.00e-13
OR combined (95% CI):1.13 (1.11-1.15)
Risk (non-risk) allele:A(C)

Allele frequencies

Proximal genes

AHI1, C6orf217, PDE7B

Links

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Region

dbSNP id:rs17066096
status:novel association
physical position:06:137,494,601
association region:06:137,348,718-137,555,201
functional tag:N/A
nearest gene:IL22RA2
candidate gene:IL22RA2

Signal

p-value discovery:3.4e-10
OR discovery (95% CI):1.14 (1.09-1.18)
p-value replication:2.10e-04 (one-sided)
OR replication (95% CI):1.14 (1.06-1.22)
p-value combined:6.00e-13
OR combined (95% CI):1.14 (1.12-1.15)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

IFNGR1, IL20RA, IL22RA2

Links

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Region

dbSNP id:rs13192841
status:previously reported
physical position:06:138,008,907
association region:06:137,915,794-138,195,369
functional tag:N/A
nearest gene:(none)
candidate gene:(none)

Signal

p-value discovery:2.3e-06
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:7.50e-04 (one-sided)
OR replication (95% CI):1.11 (1.04-1.19)
p-value combined:1.30e-08
OR combined (95% CI):1.1 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

Links

Visit the NHGRI GWAS catalog

Region

dbSNP id:rs1738074
status:novel association
physical position:06:159,385,965
association region:06:159,242,319-159,461,276
functional tag:N/A
nearest gene:TAGAP
candidate gene:TAGAP

Signal

p-value discovery:5.3e-11
OR discovery (95% CI):1.13 (1.09-1.17)
p-value replication:1.30e-05 (one-sided)
OR replication (95% CI):1.14 (1.07-1.22)
p-value combined:6.80e-15
OR combined (95% CI):1.13 (1.12-1.15)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

RSPH3, TAGAP

Links

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Region

dbSNP id:rs354033
status:novel association
physical position:07:148,920,397
association region:07:148,754,372-149,058,702
functional tag:Regulatory region (ZNF746)
nearest gene:ZNF767
candidate gene:ZNF746

Signal

p-value discovery:6.1e-06
OR discovery (95% CI):1.1 (1.06-1.15)
p-value replication:6.70e-05 (one-sided)
OR replication (95% CI):1.14 (1.07-1.22)
p-value combined:4.70e-09
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

KRBA1, ZNF746, ZNF767, ZNF777

Links

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Region

dbSNP id:rs1520333
status:previously reported
physical position:08:79,563,593
association region:08:78,828,530-79,823,754
functional tag:N/A
nearest gene:PKIA
candidate gene:IL7

Signal

p-value discovery:6.1e-07
OR discovery (95% CI):1.11 (1.06-1.15)
p-value replication:3.20e-02 (one-sided)
OR replication (95% CI):1.07 (1-1.14)
p-value combined:1.60e-07
OR combined (95% CI):1.1 (1.08-1.11)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

FAM164A, IL7, PKIA

Links

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Region

dbSNP id:rs4410871
status:novel association
physical position:08:128,884,211
association region:08:128,822,713-129,012,679
functional tag:N/A
nearest gene:PVT1
candidate gene:MYC

Signal

p-value discovery:1.7e-07
OR discovery (95% CI):1.11 (1.07-1.16)
p-value replication:6.40e-03 (one-sided)
OR replication (95% CI):1.09 (1.02-1.17)
p-value combined:7.70e-09
OR combined (95% CI):1.11 (1.09-1.12)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

MYC, PVT1

Links

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Region

dbSNP id:rs2019960
status:novel association
physical position:08:129,261,453
association region:08:129,188,889-129,366,891
functional tag:N/A
nearest gene:PVT1
candidate gene:PVT1

Signal

p-value discovery:1.4e-05
OR discovery (95% CI):1.1 (1.05-1.15)
p-value replication:1.90e-05 (one-sided)
OR replication (95% CI):1.16 (1.08-1.24)
p-value combined:5.20e-09
OR combined (95% CI):1.12 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

PVT1

Links

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Region

dbSNP id:rs3118470
status:previously reported
physical position:10:6,141,719
association region:10:6,070,200-6,235,251
functional tag:N/A
nearest gene:IL2RA
candidate gene:IL2RA

Signal

p-value discovery:2e-09
OR discovery (95% CI):1.12 (1.08-1.17)
p-value replication:1.80e-03 (one-sided)
OR replication (95% CI):1.1 (1.03-1.17)
p-value combined:3.20e-11
OR combined (95% CI):1.12 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

IL15RA, IL2RA, PFKFB3, RBM17

Links

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Region

dbSNP id:rs1250550
status:previously reported
physical position:10:80,730,323
association region:10:80,630,397-80,812,694
functional tag:N/A
nearest gene:ZMIZ1
candidate gene:ZMIZ1

Signal

p-value discovery:1.4e-06
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:5.30e-04 (one-sided)
OR replication (95% CI):1.12 (1.05-1.2)
p-value combined:6.30e-09
OR combined (95% CI):1.1 (1.09-1.12)
Risk (non-risk) allele:A(C)

Allele frequencies

Proximal genes

PPIF, ZCCHC24, ZMIZ1

Links

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Region

dbSNP id:rs7923837
status:novel association
physical position:10:94,471,897
association region:10:94,186,576-94,491,896
functional tag:N/A
nearest gene:HHEX
candidate gene:HHEX

Signal

p-value discovery:3e-07
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:2.30e-03 (one-sided)
OR replication (95% CI):1.09 (1.03-1.16)
p-value combined:4.90e-09
OR combined (95% CI):1.1 (1.08-1.11)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

HHEX, IDE, KIF11

Links

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Region

dbSNP id:rs650258
status:previously reported
physical position:11:60,588,858
association region:11:60,481,885-60,607,448
functional tag:N/A
nearest gene:CD5
candidate gene:CD6

Signal

p-value discovery:1.7e-09
OR discovery (95% CI):1.12 (1.08-1.16)
p-value replication:1.40e-03 (one-sided)
OR replication (95% CI):1.1 (1.03-1.18)
p-value combined:2.00e-11
OR combined (95% CI):1.12 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CD5, CD6, SLC15A3, TMEM132A

Links

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Region

dbSNP id:rs630923
status:strong evidence
physical position:11:118,259,563
association region:11:117,819,848-118,403,512
functional tag:N/A
nearest gene:CXCR5
candidate gene:CXCR5

Signal

p-value discovery:6.9e-06
OR discovery (95% CI):1.11 (1.06-1.17)
p-value replication:6.40e-03 (one-sided)
OR replication (95% CI):1.13 (1.03-1.24)
p-value combined:2.80e-07
OR combined (95% CI):1.12 (1.1-1.14)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

ARCN1, BCL9L, C11orf60, CCDC84, CXCR5, DDX6, FOXR1, HYOU1, MLL, PHLDB1, RPL23AP64, RPS25, SLC37A4, TMEM25, TRAPPC4, TREH, TTC36, UPK2

Links

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Region

dbSNP id:rs1800693
status:previously reported
physical position:12:6,310,270
association region:12:6,285,549-6,340,964
functional tag:N/A
nearest gene:TNFRSF1A
candidate gene:TNFRSF1A

Signal

p-value discovery:1.8e-10
OR discovery (95% CI):1.12 (1.08-1.16)
p-value replication:1.70e-05 (one-sided)
OR replication (95% CI):1.15 (1.08-1.24)
p-value combined:4.10e-14
OR combined (95% CI):1.12 (1.11-1.14)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

LTBR, PLEKHG6, SCNN1A, TNFRSF1A

Links

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Region

dbSNP id:rs10466829
status:novel association
physical position:12:9,767,358
association region:12:9,320,354-9,911,731
functional tag:Regulatory region (CLECL1)
nearest gene:CLECL1
candidate gene:CLECL1

Signal

p-value discovery:1.1e-05
OR discovery (95% CI):1.09 (1.05-1.13)
p-value replication:1.20e-04 (one-sided)
OR replication (95% CI):1.12 (1.05-1.19)
p-value combined:1.40e-08
OR combined (95% CI):1.09 (1.08-1.11)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

CD69, CLEC2B, CLEC2D, CLECL1, DDX12, KLRB1, KLRF1, LOC374443, LOC642846

Links

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Region

dbSNP id:rs12368653
status:previously reported
physical position:12:56,419,523
association region:12:55,915,445-56,893,768
functional tag:N/A
nearest gene:AGAP2
candidate gene:CYP27B1

Signal

p-value discovery:2e-07
OR discovery (95% CI):1.11 (1.06-1.15)
p-value replication:1.10e-03 (one-sided)
OR replication (95% CI):1.1 (1.03-1.16)
p-value combined:1.70e-09
OR combined (95% CI):1.1 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

AGAP2, ARHGAP9, AVIL, B4GALNT1, CDK4, CTDSP2, CYP27B1, DCTN2, DDIT3, DTX3, FAM119B, GEFT, GLI1, INHBC, INHBE, KIF5A, LOC100130776, LRP1, MARCH9, MARS, MBD6, METTL1, NDUFA4L2, NXPH4, OS9, PIP4K2C, R3HDM2, SHMT2, SLC26A10, STAC3, TSFM, TSPAN31, XRCC6BP1

Links

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Region

dbSNP id:rs949143
status:previously reported
physical position:12:122,161,116
association region:12:121,954,616-122,522,299
functional tag:Non-synonymous coding (ARL6IP4)
nearest gene:PITPNM2
candidate gene:ARL6IP4

Signal

p-value discovery:0.00015
OR discovery (95% CI):1.08 (1.04-1.12)
p-value replication:N/A?
OR replication (95% CI):N/A
p-value combined:N/A?
OR combined (95% CI):N/A
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

ABCB9, ARL6IP4, C12orf65, CDK2AP1, MPHOSPH9, OGFOD2, PITPNM2, RILPL1, RILPL2, SBNO1, SETD8, SNRNP35, VPS37B

Links

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Region

dbSNP id:rs4902647
status:novel association
physical position:14:68,323,944
association region:14:68,206,919-68,385,659
functional tag:N/A
nearest gene:ZFP36L1
candidate gene:ZFP36L1

Signal

p-value discovery:3.8e-08
OR discovery (95% CI):1.11 (1.07-1.15)
p-value replication:2.40e-05 (one-sided)
OR replication (95% CI):1.13 (1.07-1.2)
p-value combined:9.30e-12
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

ACTN1, C14orf181, ZFP36L1

Links

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Region

dbSNP id:rs2300603
status:novel association
physical position:14:75,075,310
association region:14:75,014,385-75,100,333
functional tag:N/A
nearest gene:BATF
candidate gene:BATF

Signal

p-value discovery:1.9e-07
OR discovery (95% CI):1.11 (1.07-1.16)
p-value replication:1.50e-02 (one-sided)
OR replication (95% CI):1.08 (1.01-1.16)
p-value combined:2.00e-08
OR combined (95% CI):1.11 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

BATF, FLVCR2, JDP2

Links

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Region

dbSNP id:rs2119704
status:novel association
physical position:14:87,557,442
association region:14:87,281,291-87,757,780
functional tag:Non-synonymous coding (GALC)
nearest gene:GPR65
candidate gene:GALC

Signal

p-value discovery:3.5e-10
OR discovery (95% CI):1.26 (1.17-1.36)
p-value replication:2.50e-02 (one-sided)
OR replication (95% CI):1.12 (1-1.26)
p-value combined:2.20e-10
OR combined (95% CI):1.22 (1.19-1.25)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

GALC, GPR65, KCNK10

Links

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Region

dbSNP id:rs2744148
status:strong evidence
physical position:16:1,013,553
association region:16:985,320.6-1,048,646
functional tag:N/A
nearest gene:SOX8
candidate gene:SOX8

Signal

p-value discovery:2.8e-06
OR discovery (95% CI):1.12 (1.07-1.17)
p-value replication:4.70e-03 (one-sided)
OR replication (95% CI):1.12 (1.03-1.22)
p-value combined:8.40e-08
OR combined (95% CI):1.12 (1.1-1.14)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

LMF1, LOC146336, SOX8, SSTR5

Links

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Region

dbSNP id:rs7200786
status:previously reported
physical position:16:11,085,302
association region:16:10,925,550-11,269,956
functional tag:N/A
nearest gene:CLEC16A
candidate gene:CLEC16A

Signal

p-value discovery:6.3e-14
OR discovery (95% CI):1.15 (1.11-1.2)
p-value replication:1.10e-04 (one-sided)
OR replication (95% CI):1.12 (1.06-1.19)
p-value combined:8.50e-17
OR combined (95% CI):1.15 (1.13-1.16)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

CIITA, CLEC16A, DEXI, PRM1, PRM2, PRM3, SOCS1, TNP2

Links

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Region

dbSNP id:rs13333054
status:previously reported
physical position:16:84,568,534
association region:16:84,520,930-84,580,066
functional tag:N/A
nearest gene:IRF8
candidate gene:IRF8

Signal

p-value discovery:7e-08
OR discovery (95% CI):1.12 (1.08-1.17)
p-value replication:2.70e-02 (one-sided)
OR replication (95% CI):1.09 (1-1.18)
p-value combined:1.30e-08
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

IRF8

Links

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Region

dbSNP id:rs9891119
status:previously reported
physical position:17:37,761,506
association region:17:37,571,803-38,174,639
functional tag:N/A
nearest gene:STAT3
candidate gene:STAT3

Signal

p-value discovery:4.6e-07
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:3.40e-05 (one-sided)
OR replication (95% CI):1.13 (1.07-1.2)
p-value combined:1.80e-10
OR combined (95% CI):1.11 (1.09-1.12)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

ATP6V0A1, CCR10, CNTNAP1, COASY, EZH1, FAM134C, GHDC, HCRT, HSD17B1, KCNH4, LOC100190938, MLX, NAGLU, PLEKHH3, PSMC3IP, PTRF, RAB5C, RAMP2, STAT3, STAT5A, STAT5B, TUBG1, TUBG2, VPS25, WNK4

Links

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Region

dbSNP id:rs180515
status:strong evidence
physical position:17:55,379,057
association region:17:54,783,128-55,416,497
functional tag:N/A
nearest gene:RPS6KB1
candidate gene:RPS6KB1

Signal

p-value discovery:1.4e-07
OR discovery (95% CI):1.11 (1.07-1.15)
p-value replication:5.00e-02 (one-sided)
OR replication (95% CI):1.05 (0.99-1.12)
p-value combined:8.80e-08
OR combined (95% CI):1.09 (1.08-1.11)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CLTC, DHX40, DHX40P, PTRH2, RNFT1, RPS6KB1, TMEM49, TUBD1, YPEL2

Links

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Region

dbSNP id:rs7238078
status:novel association
physical position:18:54,535,172
association region:18:54,476,982-54,681,323
functional tag:N/A
nearest gene:MALT1
candidate gene:MALT1

Signal

p-value discovery:2.2e-06
OR discovery (95% CI):1.11 (1.06-1.16)
p-value replication:1.20e-04 (one-sided)
OR replication (95% CI):1.14 (1.06-1.23)
p-value combined:2.50e-09
OR combined (95% CI):1.12 (1.1-1.14)
Risk (non-risk) allele:A(C)

Allele frequencies

Proximal genes

MALT1, ZNF532

Links

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Region

dbSNP id:rs1077667
status:novel association
physical position:19:6,619,972
association region:19:6,563,807-6,636,403
functional tag:N/A
nearest gene:TNFSF14
candidate gene:TNFSF14

Signal

p-value discovery:2.1e-12
OR discovery (95% CI):1.16 (1.11-1.21)
p-value replication:6.40e-03 (one-sided)
OR replication (95% CI):1.14 (1.03-1.27)
p-value combined:9.40e-14
OR combined (95% CI):1.16 (1.14-1.18)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

C3, CD70, TNFSF14

Links

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Region

dbSNP id:rs8112449
status:previously reported
physical position:19:10,381,064
association region:19:10,273,627-10,489,218
functional tag:N/A
nearest gene:CDC37
candidate gene:TYK2

Signal

p-value discovery:1.5e-06
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:7.90e-02 (one-sided)
OR replication (95% CI):1.05 (0.98-1.11)
p-value combined:1.20e-06
OR combined (95% CI):1.08 (1.07-1.1)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CDC37, FDX1L, GLP-1, ICAM1, ICAM3, ICAM4, ICAM5, KEAP1, PDE4A, RAVER1, S1PR5, TYK2

Links

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Region

dbSNP id:rs874628
status:novel association
physical position:19:18,165,700
association region:19:18,004,486-18,271,361
functional tag:Stop gained (MPV17L2)
nearest gene:MPV17L2
candidate gene:MPV17L2

Signal

p-value discovery:4.3e-08
OR discovery (95% CI):1.12 (1.08-1.17)
p-value replication:2.80e-02 (one-sided)
OR replication (95% CI):1.07 (1-1.14)
p-value combined:1.30e-08
OR combined (95% CI):1.11 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

ARRDC2, IFI30, IL12RB1, JUND, KIAA1683, LSM4, MAST3, MPV17L2, PDE4C, PIK3R2, RAB3A

Links

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Region

dbSNP id:rs2303759
status:novel association
physical position:19:54,560,863
association region:19:54,406,574-54,620,371
functional tag:Non-synonymous coding (DKKL1)
nearest gene:DKKL1
candidate gene:DKKL1

Signal

p-value discovery:3.8e-07
OR discovery (95% CI):1.11 (1.07-1.15)
p-value replication:2.00e-03 (one-sided)
OR replication (95% CI):1.11 (1.03-1.19)
p-value combined:5.20e-09
OR combined (95% CI):1.11 (1.09-1.13)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

CCDC155, CD37, DKKL1, PIH1D1, PTH2, SLC17A7, SLC6A16, TEAD2, TRPM4

Links

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Region

dbSNP id:rs2425752
status:previously reported
physical position:20:44,135,527
association region:20:43,965,041-44,248,988
functional tag:N/A
nearest gene:NCOA5
candidate gene:CD40

Signal

p-value discovery:1.7e-06
OR discovery (95% CI):1.1 (1.06-1.14)
p-value replication:1.90e-05 (one-sided)
OR replication (95% CI):1.15 (1.08-1.23)
p-value combined:5.10e-10
OR combined (95% CI):1.11 (1.1-1.13)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

C20orf165, CD40, CDH22, CTSA, MMP9, NCOA5, NEURL2, PCIF1, PLTP, SLC12A5, ZNF335, ZSWIM1, ZSWIM3

Links

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Region

dbSNP id:rs2248359
status:novel association
physical position:20:52,224,925
association region:20:52,201,726-52,253,768
functional tag:N/A
nearest gene:CYP24A1
candidate gene:CYP24A1

Signal

p-value discovery:5.1e-09
OR discovery (95% CI):1.12 (1.08-1.16)
p-value replication:6.30e-04 (one-sided)
OR replication (95% CI):1.11 (1.04-1.19)
p-value combined:2.50e-11
OR combined (95% CI):1.12 (1.1-1.13)
Risk (non-risk) allele:G(A)

Allele frequencies

Proximal genes

CYP24A1, PFDN4

Links

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Region

dbSNP id:rs6062314
status:strong evidence
physical position:20:61,880,157
association region:20:61,662,867-61,960,032
functional tag:N/A
nearest gene:ZBTB46
candidate gene:TNFRSF6B

Signal

p-value discovery:8.3e-07
OR discovery (95% CI):1.17 (1.1-1.25)
p-value replication:2.50e-02 (one-sided)
OR replication (95% CI):1.14 (1-1.29)
p-value combined:1.30e-07
OR combined (95% CI):1.16 (1.14-1.19)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

ARFRP1, C20orf135, C20orf195, GMEB2, LIME1, PRIC285, PTK6, RTEL1, SLC2A4RG, SRMS, STMN3, TNFRSF6B, TPD52L2, ZBTB46, ZGPAT

Links

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Region

dbSNP id:rs2283792
status:novel association
physical position:22:20,461,125
association region:22:20,229,932-20,687,848
functional tag:N/A
nearest gene:MAPK1
candidate gene:MAPK1

Signal

p-value discovery:4e-06
OR discovery (95% CI):1.09 (1.05-1.13)
p-value replication:1.30e-04 (one-sided)
OR replication (95% CI):1.12 (1.05-1.18)
p-value combined:4.70e-09
OR combined (95% CI):1.1 (1.08-1.11)
Risk (non-risk) allele:C(A)

Allele frequencies

Proximal genes

CCDC116, MAPK1, PPIL2, PPM1F, RIMBP3B, RIMBP3C, SDF2L1, TOP3B, UBE2L3, YDJC, YPEL1

Links

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Region

dbSNP id:rs140522
status:novel association
physical position:22:49,318,132
association region:22:49,279,169-49,423,510
functional tag:N/A
nearest gene:ODF3B
candidate gene:SCO2

Signal

p-value discovery:3.9e-06
OR discovery (95% CI):1.09 (1.05-1.14)
p-value replication:4.90e-04 (one-sided)
OR replication (95% CI):1.12 (1.05-1.2)
p-value combined:1.70e-08
OR combined (95% CI):1.1 (1.09-1.12)
Risk (non-risk) allele:A(G)

Allele frequencies

Proximal genes

ADM2, ARSA, C22orf41, CHKB, CPT1B, KLHDC7B, LMF2, LOC100144603, MAPK8IP2, MIOX, NCAPH2, ODF3B, SBF1, SCO2, TYMP

Links

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Left panels: interval of ±100kb flanking the association region of the lead SNP in the chosen region. Positions are in megabases along the chromosome, in NCBI build 36 coordinates. The top panel shows the -log10(p-value), truncated at a maximum of 10 where relevant, for all SNPs within this interval. SNPs are coloured by r2 (estimated from the 58C control cohort genotypes) with the lead SNP, according to the legend in the top left corner. SNPs represented with a black dot have r2 < 0.01 The bottom panel shows the recombination rate from the HapMap phase II recombination map, and all genes in the interval. The boundaries of the association region are depicted by red dashed vertical lines. Right panels: allele intensity cluster plots for the lead SNP are shown for each of the MS internal ("MSCCC2"), 58C ("58C"), UK National Blood Service ("UKBS"), and MS external ("MS_ext") datasets.

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