Variant report

Variant	rs1632958
Chromosome Location	chr6:29688643-29688644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:29688599-29689013	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZEB1	chr6:29688589-29688889	GM12878	blood:	n/a	chr6:29688775-29688784
3	RAD21	chr6:29688520-29689076	HCT-116	colon:	n/a	n/a
4	CTCF	chr6:29688602-29689121	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29681737..29685555-chr6:29686615..29688782,3	MCF-7	breast:
2	chr6:29683436..29685775-chr6:29686962..29689399,3	K562	blood:
3	chr6:29686730..29689127-chr6:29696614..29698519,2	K562	blood:

Variant related genes	Relation type
HLA-F	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1059174	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610600	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610603	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610604	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610605	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610607	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610613	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610623	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1610626	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610627	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610630	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610632	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610727	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1610728	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610737	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610738	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610740	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1611278	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1611279	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611292	0.86[EUR][1000 genomes]
rs1611293	0.84[EUR][1000 genomes]
rs1611294	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611297	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611352	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625607	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625636	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626636	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632447	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632956	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632959	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633012	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1633025	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633026	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633036	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633038	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633042	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633043	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633045	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633046	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633048	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633049	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633050	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633051	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633052	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633055	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633056	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633057	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633058	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633060	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633061	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633062	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633064	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633069	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633070	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633071	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633074	0.93[ASN][1000 genomes]
rs1633076	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633091	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736910	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736911	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1736914	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736916	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736921	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736995	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1737008	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1737022	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1737039	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1737058	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1737060	0.83[EUR][1000 genomes]
rs1737065	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737066	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737067	0.84[EUR][1000 genomes]
rs1737068	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737070	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737071	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737073	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737074	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737075	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737079	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1737081	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737084	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737087	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248693	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735050	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117297	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3117303	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129081	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129184	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130252	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131858	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131862	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3135049	0.81[EUR][1000 genomes]
rs3135050	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6933762	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733840	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733841	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909717	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909723	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909724	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs909725	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs909726	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909727	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909732	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909735	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258243	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932338	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932341	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs1632958	HLA-A	cis	lung	GTEx
rs1632958	HLA-A	cis	Whole Blood	GTEx
rs1632958	HLA-A	cis	Thyroid	GTEx
rs1632958	HCG4P5	cis	Nerve Tibial	GTEx
rs1632958	HCG4P5	cis	Whole Blood	GTEx
rs1632958	HCG4P5	cis	Muscle Skeletal	GTEx
rs1632958	HLA-A	cis	Skin Sun Exposed Lower leg	GTEx
rs1632958	HLA-A	cis	Artery Tibial	GTEx
rs1632958	HCG4P5	cis	Adipose Subcutaneous	GTEx
rs1632958	HLA-K	cis	Artery Aorta	GTEx
rs1632958	HCG4P5	cis	Esophagus Muscularis	GTEx
rs1632958	HCG4P5	cis	Artery Tibial	GTEx
rs1632958	HCG4P5	cis	Heart Left Ventricle	GTEx
rs1632958	HLA-K	cis	lung	GTEx
rs1632958	HCG4P5	cis	Thyroid	GTEx
rs1632958	HLA-J	cis	Muscle Skeletal	GTEx
rs1632958	HCG4P5	cis	lung	GTEx
rs1632958	HLA-J	cis	Whole Blood	GTEx
rs1632958	HLA-A	cis	Muscle Skeletal	GTEx
rs1632958	HLA-A	cis	Heart Left Ventricle	GTEx
rs1632958	HLA-A	cis	Esophagus Muscularis	GTEx
rs1632958	HLA-A	cis	Adipose Subcutaneous	GTEx
rs1632958	HCG4P5	cis	Skin Sun Exposed Lower leg	GTEx
rs1632958	HLA-K	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29678600-29689200	Weak transcription	GM12878-XiMat	blood
3	chr6:29688200-29689200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:29688200-29689800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:29688200-29689800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr6:29688200-29690400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:29688400-29690200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:29688400-29690200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:29688400-29690200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr6:29688400-29690400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:29688600-29688800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
12	chr6:29688600-29688800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr6:29688600-29688800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:29688600-29689200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:29688600-29689600	Enhancers	Primary T cells from cord blood	blood
16	chr6:29688600-29689800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:29688600-29690800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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