Variant report

Variant	rs1632957
Chromosome Location	chr6:29688667-29688668
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	CTCF	chr6:29688666-29688938	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:29688653-29689024	GM12878	blood:	n/a	n/a
3	RAD21	chr6:29688599-29689013	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZEB1	chr6:29688589-29688889	GM12878	blood:	n/a	chr6:29688775-29688784
5	RAD21	chr6:29688520-29689076	HCT-116	colon:	n/a	n/a
6	ZNF143	chr6:29688666-29688987	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr6:29688652-29689041	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr6:29688657-29688991	H1-hESC	embryonic stem cell:	n/a	n/a
9	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: 51 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1419696	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1610588	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1610601	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1610602	0.85[ASN][1000 genomes]
rs1610608	0.83[ASN][1000 genomes]
rs1610612	0.85[ASN][1000 genomes]
rs1610617	0.82[ASN][1000 genomes]
rs1610621	0.85[ASN][1000 genomes]
rs1610625	0.80[ASN][1000 genomes]
rs1610629	0.83[ASN][1000 genomes]
rs1610633	0.84[ASN][1000 genomes]
rs1610729	0.85[ASN][1000 genomes]
rs1610735	0.81[ASN][1000 genomes]
rs1610742	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1610744	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1628578	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1632960	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1633063	0.85[ASN][1000 genomes]
rs1633065	0.81[ASN][1000 genomes]
rs1633088	0.83[ASN][1000 genomes]
rs1633096	0.85[ASN][1000 genomes]
rs1633098	0.85[ASN][1000 genomes]
rs1633099	0.85[ASN][1000 genomes]
rs1633106	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1633107	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736915	0.85[ASN][1000 genomes]
rs1737077	0.85[ASN][1000 genomes]
rs2517910	0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2517911	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3094730	0.86[EUR][1000 genomes]
rs3094731	0.86[EUR][1000 genomes]
rs3129046	0.85[EUR][1000 genomes]
rs3131864	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131867	0.86[EUR][1000 genomes]
rs885942	0.85[ASN][1000 genomes]
rs885943	0.85[ASN][1000 genomes]
rs885944	0.85[ASN][1000 genomes]
rs885945	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs885946	0.85[ASN][1000 genomes]
rs9258068	0.84[EUR][1000 genomes]
rs929158	0.85[ASN][1000 genomes]
rs929159	0.85[ASN][1000 genomes]
rs929160	0.86[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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1632957	HIST1H2BM	cis	cerebellum	SCAN
rs1632957	ZFP57	cis	Skin Sun Exposed Lower leg	GTEx
rs1632957	ZFP57	cis	Heart Left Ventricle	GTEx
rs1632957	ZFP57	cis	Adipose Subcutaneous	GTEx
rs1632957	ZNF323	cis	parietal	SCAN
rs1632957	ZFP57	cis	Esophagus Mucosa	GTEx
rs1632957	HIST1H3I	cis	cerebellum	SCAN
rs1632957	IFITM4P	cis	Thyroid	GTEx
rs1632957	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1632957	HLA-F-AS1	cis	Whole Blood	GTEx
rs1632957	ZFP57	cis	Nerve Tibial	GTEx
rs1632957	ZFP57	cis	Thyroid	GTEx
rs1632957	HLA-G	cis	multi-tissue	Pritchard
rs1632957	ZFP57	cis	Whole Blood	GTEx
rs1632957	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1632957	HLA-A	cis	lymphoblastoid	seeQTL
rs1632957	ZNRD1-AS1	cis	Nerve Tibial	GTEx
rs1632957	ZFP57	cis	Artery Tibial	GTEx
rs1632957	ZKSCAN3	cis	parietal	SCAN
rs1632957	ZFP57	cis	lung	GTEx
rs1632957	HLA-G	cis	lymphoblastoid	seeQTL
rs1632957	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

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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