Table I. List of reported T1D SNPs located in 59 non-HLA T1D loci
IDLocusT1D SNPChrBPGenep ValueRef.Tables
11p31.3rs2269241Chr 163881359PGM14.00 × 10−7(2)II, S
21p13.2rs2476601Chr 1114179091PTPN228.50 × 10−85(2)II
31q31.2rs2816316Chr 1190803436RGS13.10 × 10−5a(2)
41q32.1rs3024493Chr 1205010591IL101.90 × 10−9(2)
52p24.3rs1534422Chr 212558192Intergenic2.00 × 10−6(2)IV
62p23.3rs2165738Chr 224546313Intergenic4.00 × 10−6(14)III, S
72p13.1rs363609^Chr 274756380DQX18.53 × 10−6b(15)II, III, S
82q11.2rs9653442Chr 2100191799AFF35.00 × 10−6(15)S
92q12.1rs6543134Chr 2102416890IL18RAP8.03 × 10−5a(16)III, S
102q24.2rs1990760Chr 2162832297IFIH16.60 × 10−9(2)II, IV
2q24.2rs3747517Chr 2162837070IFIH14.70 × 10−7(2)
112q33.2rs11571291Chr 2204429377CTLA41.19 × 10−12(17)IV
2q33.2rs3087243Chr 2204447164CTLA41.20 × 10−15(2)
2q33.2rs231727Chr 2204449795CTLA42.13 × 10−18(13)II, S
122q35rs3731865Chr 2218958247SLC11A11.55 × 10−6(18)III
133p21.31rs11711054Chr 346320615CCR51.70 × 10−5a(2)IV
144p15.2rs10517086Chr 425694609Intergenic4.60 × 10−10(2)
154q27rs4505848Chr 4123351942IL24.70 × 10−13(2)
4q27rs17388568Chr 4123548812IL23.00 × 10−6(19)
4q27rs2069763Chr 4123596932IL21.91 × 10−10(13)
165p13.2rs6897932Chr 535910332IL7R8.00 × 10−6(15)II
176q15rs597325Chr 691059215BACH23.38 × 10−10(17)S
6q15rs56297233Chr 691070750BACH25.40 × 10−8(2)III
186q22.32rs9388489Chr 6126740412C6orf1734.20 × 10−13(2)III
196q23.3rs2327832Chr 6138014761TNFAIP31.60 × 10−4a(2)S
6q23.3rs10499194Chr 6138044330TNFAIP33.00 × 10−4a(2)III, IV
206q25.3rs1738074Chr 6159385965TAGAP7.59 × 10−9(16)S
217p15.2rs7804356Chr 726858190Intergenic5.30 × 10−9(2)III, IV
227p12.2rs10272724Chr 750444707IKZF14.80 × 10−9(20)III
239p24.2rs7020673Chr 94281747GLIS35.40 × 10−12(2)IV, S
9p24.2rs10758593Chr 94282083GLIS31.18 × 10−8(17)S
2410p15.1rs12251307Chr 106163501IL2RA1.30 × 10−13(2)IV
2510p15.1rs947474Chr 106430456PRKCQ4.00 × 10−9(14)IV, S
10p15.1rs11258747Chr 106512897PRKCQ1.20 × 10−7(2)
2610p11.22rs722988Chr 1033466153NRP14.88 × 10−8(21)S
2710q23.31rs10509540Chr 1090013013C10orf591.30 × 10−28(2)III, S
2811p15.5rs7928968Chr 112006875INS2.78 × 10−14(17)
11p15.5rs3842727Chr 112141424TH4.89 × 10−196(13)IV
11p15.5rs7111341Chr 112169742INS4.40 × 10−48(2)
2912p13.31rs3764021Chr 129724895NR5.00 × 10−8(19)III, S
12p13.31rs10466829Chr 129767358CLECL19.19 × 10−9(17)III, S
12p13.31rs4763879Chr 129801431CD691.90 × 10−11(2)
3012q13.2rs705704Chr 1254721679ERBB34.31 × 10−31(17)III, IV, S
12q13.2rs11171739Chr 1254756892ERBB31.00 × 10−11(19)
12q13.2rs2292239Chr 1254768447ERBB32.20 × 10−25(2)III, S
3112q13.3rs3809114Chr 1256134906NR6.90 × 10−4a(2)
3212q14.1rs10877012Chr 1256448352CYP27B13.80 × 10−6(22)II, III, S
3312q24.12rs1265565Chr 12110199580CUX21.00 × 10−16(23)IV, S
12q24.12rs3184504Chr 12110368991SH2B32.80 × 10−27(2)II
3412q24.13rs17696736Chr 12110971201C12orf301.73 × 10−13(15)IV, S
3513q32.3rs9585056Chr 1398879767GPR1835.20 × 10−9(24)IV
3614q24.1rs1465788Chr 1468333352Intergenic1.80 × 10−12(2)
3714q32.2rs4900384Chr 1497568704Intergenic3.70 × 10−9(2)
3814q32.2rs56994090Chr 14100376200DLK11.62 × 10−10(25)
3915q14rs17574546Chr 1536689768RASGRP13.35 × 10−8(13)III
15q14rs12908309Chr 1536715969RASGRP14.31 × 10−8(17)IV
4015q25.1rs3825932Chr 1577022501CTSH7.70 × 10−8(2)II–IV
4116p13.13rs12708716Chr 1611087374CLEC16A2.20 × 10−16(2)
16p13.13rs12927355Chr 1611102272DEXI1.91 × 10−16(17)
16p13.13rs416603Chr 1611271580C16orf753.00 × 10−6(14)II–IV
4216p11.2rs4788084Chr 1628447349IL272.60 × 10−13(2)II, III, S
16p11.2rs9924471Chr 1628499031IL271.21 × 10−11(17)II
4316q23.1rs7202877Chr 1673804746Intergenic3.10 × 10−15(2)
16q23.1rs8056814Chr 1673809828NR1.13 × 10−7(17)
4417p13.1rs16956936Chr 177574417Intergenic5.00 × 10−7(2)
4517q12rs2290400Chr 1735319766ORMDL35.50 × 10−13(2)II–IV, S
4617q21.2rs7221109Chr 1736023812Intergenic1.30 × 10−9(2)III, IV, S
4718p11.21rs1893217Chr 1812799340PTPN23.60 × 10−15(2)IV, S
4818q22.2rs763361Chr 1865682622CD2261.56 × 10−8(16)II, III, IV
4919p13.2rs2304256Chr 1910336652TYK24.13 × 10−9(25)II, IV, S
5019q13.32rs425105Chr 1951900321Intergenic2.70 × 10−11(2)IV
5119q13.33rs679574Chr 1953897920FUT24.30 × 10−18(16)IV, S
5220p13rs2281808Chr 201558551Intergenic1.20 × 10−11(2)II
5321q22.3rs11203203Chr 2142709255UBASH3A1.70 × 10−9(2)III, S
21q22.3rs876498Chr 2142714896UBASH3A7.06 × 10−9(13)IV
5422q12.2rs5753037Chr 2228911722Intergenic2.60 × 10−16(2)III, S
5522q12.3rs229541Chr 2235921264C1QTNF62.10 × 10−7(2)II, S
Four Newly Discovered Loci
561q32.1rs6691977Chr 1200814959NR4.30 × 10−8(13)
572q13rs4849135Chr 2111615079NR4.40 × 10−8(13)
584q32.3rs2611215Chr 4166574267NR1.80 × 10−11(13)S
595p13.2rs11954020Chr 535883251IL7R4.40 × 10−8(13)
  • In the Tables column, II, III, IV, and S correspond to tables where SNPs are featured; that is, II, nonsynonymous LD SNPs; III, cis- interacting genes; IV, trans-interacting genes; S, supplementary cis-interacting genes (see Supplemental Table IIi).

  • a The p value is derived from table II in Barrett et al. (2).

  • b rs363609 is in LD with reported SNP rs6546909 (r2 = 0.84) whose p value is stated.

  • BP, NCBI36 chromosome positions; ID, unique T1D loci identifier; NR, no gene of interest was reported at the locus; Ref., publication reference.