Overview

2,861 primary billiary cirrhosis cases from UK PBC Consortium and 8,514 UK controls were genotyped using iSelect Illumina Infinium array (ImmunoChip), optiCall was used to call variants. Imputation, in order to include additional genotypes was carried out using data from 1000 genomes project and computed using IMPUTE2. Association statistics were calculated using PLINK v1.07. In total 16 known (including MHC) and three novel loci were reported (P < 5 x 10-8)

Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryPBC28618514--
Exclusion Criteria

SNPs with the following properties were excluded from analysis.

  • Monomorphic.
  • HWE P < 1 x 10-6.
  • MAF < 0.1.
  • Call rate > 98% or call rate between case/control significanly different (P < 10-5).

Samples with the following properties were excluded from analysis

  • < 98% call rate 
  • heterozygosity > 3 s.d. from the mean.
  • For samples with IBD > 18.75% sample with lower call rate removed.
  • Non-european ancestry.

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p31.3chr1:67297383-67475484IL12RB2  rs72678531T > C0.1702.47e-38C1.61 (1.49-1.73)C
1q31.3chr1:197342098-197969200DENND1B  rs2488393C > T0.2104.29e-12C1.28 (1.19-1.37)C
2q32.3chr2:190995776-191143008STAT4  STAT1  rs7574865G > T0.2201.38e-13C1.31 (1.22-1.40)C
2q32.3chr2:190990148-191143008STAT4  STAT1  rs3024921A > T0.0602.59e-18C1.62 (1.45-1.80)C
3q13.33chr3:119384793-119581808TIMMDC1  TMEM39A  POGLUT1  CD80  rs2293370G > A0.2006.84e-16C1.39 (1.28-1.52)C
3q25.33chr3:159855940-160002484IL12A  rs62270414T > C0.1505.74e-17C1.41 (1.30-1.53)C
3q25.33chr3:159906172-160041614IL12A  rs668998A > G0.4304.73e-09C1.26 (1.17-1.36)C
3q25.33chr3:159840164-160002484IL12A  rs80014155C > T0.0042.64e-11C3.44 (2.39-4.94)C
3q25.33chr3:159973324-160104880IL12A  rs2366643T > C0.4303.92e-22C1.35 (1.27-1.45)C
4q24chr4:102467408-103205026MANBA  NFKB1  rs7665090G > A0.4808.48e-14C1.27 (1.19-1.33)C
5p13.2chr5:35798580-36036080UGT3A1  CAPSL  IL7R  SPEF2  rs6871748T > C0.2802.26e-13C1.3 (1.2-1.41)C
7q32.1chr7:128911686-129138653IRF5  TNPO3  rs35188261G > A0.1706.52e-22C1.52 (1.39-1.63)C
7q32.1chr7:128911686-129137466IRF5  TNPO3  rs3807307T > C0.4704.12e-09C1.22 (1.14-1.30)C
11q23.3chr11:118490430-118916120DDX6  rs10607450T > C0.2107.20e-16C1.39 (1.28-1.49)C
12p13.31chr12:6373620-6414083SCNN1A  TNFRSF1A  LTBR  rs11064157C > A0.2501.69e-09C1.23 (1.15-1.32)C
12p13.31chr12:6312329-6354696SCNN1A  TNFRSF1A  LTBR  rs1800693T > C0.4001.18e-14C1.27 (1.19-1.34)C
12q24.12chr12:111287381-112592683BRAP  ATXN2  SH2B3  rs11065979C > T0.4402.87e-09C1.20 (1.13-1.27)C
14q24.1chr14:68071518-68485527RAD51B  rs911263T > C0.2909.95e-11C1.27 (1.18-1.35)C
16p13.13chr16:10923201-11218316PRM2  SOCS1  PRM1  CLEC16A  rs12708715C > T0.3202.19e-13C1.28 (1.2-1.39)C
16p13.13chr16:11193176-11372654PRM2  SOCS1  PRM1  CLEC16A  rs1646019C > T0.2906.72e-15C1.32 (1.23-1.41)C
16p13.13chr16:11210761-11381471PRM2  SOCS1  PRM1  CLEC16A  rs80073729G > A0.0042.69e-08C2.96 (2.02-4.33)C
16q24.1chr16:85958099-85990498IRF8  rs11117433G > C0.2301.41e-09C1.27 (1.18-1.35)C
17q12chr17:39226421-40083963GSDMB  ZPBP2  ORMDL3  IKZF3  rs8067378A > G0.4806.05e-14C1.27 (1.19-1.33)C
17q21.31chr17:45852834-46003698CRHR1  MAPT  rs17564829T > C0.2402.15e-09C1.25 (1.16-1.35)C
19p13.2chr19:10280033-10517872TYK2  rs34536443G > C0.0501.23e-12C1.92 (1.59-2.27)C
22q13.1chr22:39259042-39371656PDGFB  SYNGR1  RPL3  rs2267407G > A0.2301.29e-13C1.29 (1.21-1.38)C

Criteria

GDXHsS00020 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date