Variant report

Variant	rs4687614
Chromosome Location	chr3:52492085-52492086
allele	A/G
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	POLR2A	chr3:52491058-52492925	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
2	chr2:143701599..143702362-chr3:52492018..52492705,2	MCF-7	breast:
3	chr3:52487901..52490154-chr3:52491189..52493164,2	K562	blood:
4	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000168273	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000114854	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1011062	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1035003	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077142	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10865972	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707864	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs123598	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13071708	1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13074649	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[JPT][hapmap]
rs13089892	1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs1541495	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2109558	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2109559	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335640	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2335928	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs34762015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34827613	0.84[AMR][1000 genomes]
rs352141	0.84[AMR][1000 genomes]
rs35860312	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3755810	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap]
rs419050	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs419604	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs419752	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4312651	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	0.83[EUR][1000 genomes]
rs4687544	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4687617	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687618	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs575476	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap]
rs634382	1.00[JPT][hapmap]
rs6414568	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445483	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs676034	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6787493	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.84[AMR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs758800	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs758803	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968588	0.85[AMR][1000 genomes]
rs9813489	0.90[LWK][hapmap]
rs9813653	1.00[YRI][hapmap]
rs9815559	1.00[YRI][hapmap]
rs9834363	1.00[YRI][hapmap]
rs9834919	0.90[LWK][hapmap]
rs9836166	1.00[YRI][hapmap]
rs9842960	1.00[YRI][hapmap]
rs9843055	1.00[YRI][hapmap]
rs9844178	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs9844183	1.00[JPT][hapmap]
rs9845752	1.00[YRI][hapmap]
rs9846089	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850471	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4687614	STAB1	cis	multi-tissue	Pritchard
rs4687614	FLJ12442	cis	multi-tissue	Pritchard
rs4687614	ITIH4	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52490200-52492600	Flanking Active TSS	HMEC	breast
2	chr3:52490600-52492200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:52490800-52492200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:52490800-52492400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:52490800-52492400	Weak transcription	Ovary	ovary
6	chr3:52490800-52492400	Weak transcription	Psoas Muscle	Psoas
7	chr3:52490800-52492800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52490800-52492800	Weak transcription	Aorta	Aorta
9	chr3:52490800-52499200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:52491000-52492400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:52491000-52492400	Weak transcription	A549	lung
12	chr3:52491000-52492800	Weak transcription	Pancreas	Pancrea
13	chr3:52491000-52493200	Genic enhancers	Fetal Thymus	thymus
14	chr3:52491200-52492200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:52491200-52492400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:52491200-52492600	Genic enhancers	Brain Cingulate Gyrus	brain
17	chr3:52491200-52492800	Weak transcription	Colonic Mucosa	Colon
18	chr3:52491200-52493000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:52491200-52493200	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr3:52491200-52493400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:52491200-52493600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:52491200-52498800	Strong transcription	Primary T cells from cord blood	blood
23	chr3:52491400-52492200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:52491400-52492200	Genic enhancers	HUVEC	blood vessel
25	chr3:52491400-52492400	Genic enhancers	Rectal Mucosa Donor 29	rectum
26	chr3:52491400-52495400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:52491400-52497200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52491400-52500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:52491400-52501600	Weak transcription	Right Atrium	heart
30	chr3:52491400-52502200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:52491600-52492400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:52491600-52492400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:52491600-52492400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:52491600-52492600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:52491600-52492800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:52491600-52493600	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr3:52491600-52493600	Strong transcription	NHLF	lung
38	chr3:52491600-52493800	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr3:52491600-52495400	Strong transcription	Fetal Lung	lung
40	chr3:52491600-52496800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:52491600-52499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:52491600-52500000	Strong transcription	Fetal Intestine Large	intestine
43	chr3:52491600-52500600	Strong transcription	Fetal Intestine Small	intestine
44	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
45	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
46	chr3:52491800-52492200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:52491800-52492200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:52491800-52492200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:52491800-52492400	Weak transcription	Spleen	Spleen
50	chr3:52491800-52492600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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