Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

McGovern, Amanda; Schoenfelder, Stefan; Martin, Paul; Massey, Jonathan; Duffus, Kate; Plant, Darren; Yarwood, Annie; Pratt, Arthur G.; Anderson, Amy E.; Isaacs, John D.; Diboll, Julie; Thalayasingam, Nishanthi; Ospelt, Caroline; Barton, Anne; Worthington, Jane; Fraser, Peter; Eyre, Stephen; Orozco, Gisela

doi:10.1186/s13059-016-1078-x

Table 1 Functional annotation of SNPs in the 6q23 intergenic LD block tagged by rs6920220 using Haploregv4.1

From: Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

pos (hg19)	LD (r²)	Variant	Ref	Alt	AFR freq	AMR freq	EUR freq	SiPhy cons	Promoter histone marks	Enhancer histone marks	DNAse	Proteins bound	Motifs changed
chr6:137959235	0.89	rs6933404	T	C	0.11	0.11	0.17			Blood^a	GI^b		STAT
chr6:137964697	0.88	rs62432712	A	G	0.08	0.10	0.17						Pax7,RORalpha1,Vax2
chr6:137973068	0.93	rs2327832	A	G	0.11	0.11	0.17			5 tissues^c	GI,GI,PLCNT^d		10 altered motifs^e
chr6:137973832	0.92	rs928722	C	T	0.11	0.11	0.17			GI, PLCNT, LIV^f			4 altered motifs^g
chr6:137999562	0.84	rs35926684	GA	G	0.14	0.12	0.18			BLD^h			4 altered motifsⁱ
chr6:138002175	1	rs6927172	C	G	0.12	0.10	0.17	Yes	4 tissues^j	7 tissues^k	14 tissues^l	13 bound proteins^m	8 altered motifsⁿ
chr6:138003822	1	rs11757201	G	C	0.08	0.10	0.17						Mrg,Sp4
chr6:138005515	1	rs17264332	A	G	0.12	0.10	0.17			BLD^o			5 altered motifs^p
chr6:138006504	1	rs6920220	G	A	0.12	0.10	0.17						Hltf

The following settings were used: LD threshold, r² ≥ 0.8; 1000G Phase 1 population for LD calculation: EUR; Source for epigenomes: ChromHMM (25-state model using 12 imputed marks); Mammalian conservation algorithm: SiPhy-omega
^aDnd41 TCellLeukemia cell line
^bSmall intestine
^cFetal intestine small, fetal intestine large, rectal mucosa donor 31, duodenum mucosa, small intestine, rectal mucosa donor 29, stomach mucosa, placenta, fetal muscle leg, duodenum smooth muscle, fetal stomach, sigmoid colon, colonic mucosa, fetal adrenal gland, HepG2 hepatocellular carcinoma cell line
^dFetal intestine large, fetal intestine small, placenta
^eBCL, GR, HDAC2, Irf, Nanog, Pou1f1, Pou2f2, RXRA, STAT, P300
^fDuodenum mucosa, fetal intestine large, fetal intestine small, placenta, rectal mucosa donor 31, small intestine, stomach mucosa, HepG2 hepatocellular carcinoma cell line
^gBCL, NRSF, Smad, Whn
^hPrimary monocytes from peripheral blood, primary neutrophils from peripheral blood, primary B cells from cord blood, primary T helper cells PMA-I stimulated, primary T helper 17 cells PMA-I stimulated, GM12878 lymphoblastoid cells, monocytes-CD14+ RO01746 cells
ⁱCIZ, Foxd3, HDAC2, Nanog
^jPrimary T helper naïve cells from peripheral blood, primary B cells from peripheral blood, primary natural killer cells from peripheral blood, primary hematopoietic stem cells G-CSF-mobilised female, primary hematopoietic stem cells short-term culture, adipose nuclei, duodenum smooth muscle, colon smooth muscle, rectal mucosa donor 29, stomach mucosa, duodenum mucosa, liver
^kA549 EtOH 0.02 pct lung carcinoma cell line, HeLa-S3 cervical carcinoma cell line, primary mononuclear cells from peripheral blood, primary T cells effector/memory enriched from peripheral blood, primary T cells from cord blood, primary T regulatory cells from peripheral blood, primary T helper cells from peripheral blood, primary T helper cells PMA-I stimulated, primary T helper 17 cells PMA-I stimulated, primary T helper memory cells from peripheral blood 1, primary T helper memory cells from peripheral blood 2, primary T CD8+ memory cells from peripheral blood, primary T helper naïve cells from peripheral blood, primary T CD8+ naïve cells from peripheral blood, primary monocytes from peripheral blood, primary B cells from cord blood, primary hematopoietic stem cells, primary hematopoietic stem cells G-CSF-mobilised male, primary neutrophils from peripheral blood, bone marrow derived cultured mesenchymal stem cells, Dnd41 TCellLeukemia cell line, GM12878 lymphoblastoid cells, HUVEC umbilical vein endothelial primary cells, monocytes-CD14+ RO01746 primary cells, osteoblast primary cells, mesenchymal stem cell derived adipocyte cultured cells
^lA549 EtOH 0.02 pct lung carcinoma cell line, HeLa-S3 cervical carcinoma cell line, primary monocytes from peripheral blood, GM12878 lymphoblastoid cells, HUVEC umbilical vein endothelial primary cells, monocytes-CD14+ RO01746 primary cells, foreskin fibroblast primary cells skin01, HSMM cell derived skeletal muscle myotubes cells, primary hematopoietic stem cells G-CSF-mobilised female, primary B cells from peripheral blood, H1 derived mesenchymal stem cells, foreskin fibroblast primary cells skin02, foreskin keratinocyte primary cells skin02, HSMM skeletal muscle myoblasts cells
^mGR (A549), ERALPHA_A (ECC-1), IRF4 (GM12878), CFOS (HUVEC), CJUN (HUVEC), GATA2 (HUVEC), CEBPB (HeLa-S3), JUND (HeLa-S3), P300 (HeLa-S3), STAT1 (HeLa-S3), MAFK (K562), STAT3 (MCF10A-Er-Src), KAP1 (U2OS)
ⁿBCL, ERalpha-a, Ets, LXR, NFkB, RORalpha1, RXRA, STAT
^oDnd41 TCellLeukemia cell line
^pFoxp1, HDAC2, Hoxa10, Hoxa9, Hoxd10

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