Variant report

Variant	rs1541495
Chromosome Location	chr3:52492707-52492708
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	RUNX3	chr3:52492701-52493583	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52491058-52492925	K562	blood:	n/a	n/a
3	RUNX3	chr3:52492690-52493564	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52492633..52495296-chr3:52719362..52721051,2	MCF-7	breast:
2	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
3	chr3:52487901..52490154-chr3:52491189..52493164,2	K562	blood:

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000163939	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1011062	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs1011063	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1011064	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1035002	0.89[EUR][1000 genomes]
rs1035003	0.91[EUR][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs10865972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123598	1.00[JPT][hapmap]
rs123602	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13074649	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109558	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109559	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159607	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2215466	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	0.89[EUR][1000 genomes]
rs2335929	0.91[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34261027	1.00[ASN][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs35860312	1.00[JPT][hapmap]
rs3755810	0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs3774409	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap]
rs390802	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs409803	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687541	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687543	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687544	0.91[EUR][1000 genomes]
rs4687614	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]
rs4687616	0.82[EUR][1000 genomes]
rs4687617	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687618	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4687619	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4687621	0.91[EUR][1000 genomes]
rs498778	1.00[JPT][hapmap]
rs498946	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs613519	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs634382	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6414568	0.91[EUR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445484	0.91[EUR][1000 genomes]
rs6445485	0.91[EUR][1000 genomes]
rs6445486	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6445506	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676034	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6782162	0.91[EUR][1000 genomes]
rs6784615	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787493	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6810027	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs728408	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758800	0.82[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs758803	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs7620015	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887515	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929528	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs929529	0.89[EUR][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	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9847332	0.91[EUR][1000 genomes]
rs9850471	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9855470	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9863753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9867823	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52490800-52492800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52490800-52492800	Weak transcription	Aorta	Aorta
3	chr3:52490800-52499200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:52491000-52492800	Weak transcription	Pancreas	Pancrea
5	chr3:52491000-52493200	Genic enhancers	Fetal Thymus	thymus
6	chr3:52491200-52492800	Weak transcription	Colonic Mucosa	Colon
7	chr3:52491200-52493000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:52491200-52493200	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr3:52491200-52493400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:52491200-52493600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:52491200-52498800	Strong transcription	Primary T cells from cord blood	blood
12	chr3:52491400-52495400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:52491400-52497200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:52491400-52500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:52491400-52501600	Weak transcription	Right Atrium	heart
16	chr3:52491400-52502200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:52491600-52492800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:52491600-52493600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr3:52491600-52493600	Strong transcription	NHLF	lung
20	chr3:52491600-52493800	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr3:52491600-52495400	Strong transcription	Fetal Lung	lung
22	chr3:52491600-52496800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:52491600-52499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:52491600-52500000	Strong transcription	Fetal Intestine Large	intestine
25	chr3:52491600-52500600	Strong transcription	Fetal Intestine Small	intestine
26	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
27	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
28	chr3:52491800-52492800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:52491800-52492800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:52491800-52492800	Genic enhancers	Brain Germinal Matrix	brain
31	chr3:52491800-52492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:52491800-52493000	Weak transcription	Fetal Brain Male	brain
33	chr3:52491800-52493000	Genic enhancers	Dnd41	blood
34	chr3:52491800-52493200	Strong transcription	Primary B cells from cord blood	blood
35	chr3:52491800-52493400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr3:52491800-52493400	Strong transcription	Hela-S3	cervix
37	chr3:52491800-52493400	Strong transcription	HSMM	muscle
38	chr3:52491800-52493600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr3:52491800-52493600	Strong transcription	NH-A	brain
40	chr3:52491800-52493800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52491800-52493800	Strong transcription	Right Ventricle	heart
42	chr3:52491800-52493800	Strong transcription	HepG2	liver
43	chr3:52491800-52494000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:52491800-52495000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:52491800-52495400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:52491800-52495400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52491800-52495400	Strong transcription	Adipose Nuclei	Adipose
48	chr3:52491800-52495400	Strong transcription	Fetal Kidney	kidney
49	chr3:52491800-52495400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:52491800-52495600	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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