Variant report

Variant	rs658087
Chromosome Location	chr6:33665020-33665021
allele	A/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	MYC	chr6:33664827-33665270	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:33664839-33665114	MCF10A-Er-Src	breast:	n/a	chr6:33664929-33664939 chr6:33664929-33664939 chr6:33664929-33664939
3	GATA2	chr6:33664642-33665471	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr6:33664299-33665069	K562	blood:	n/a	n/a
5	FOS	chr6:33664807-33665146	MCF10A-Er-Src	breast:	n/a	chr6:33664929-33664939 chr6:33664929-33664939 chr6:33664929-33664939
6	MYC	chr6:33664807-33665232	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr6:33664715-33665176	MCF-7	breast:	n/a	n/a
8	USF2	chr6:33664788-33665362	Hela-S3	cervix:	n/a	chr6:33664814-33664830
9	POLR2A	chr6:33664619-33665363	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr6:33664702-33665403	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr6:33664885-33665085	Hela-S3	cervix:	n/a	n/a
12	TCF7L2	chr6:33664468-33665176	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:33662026-33666005	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:33664689-33665098	K562	blood:	n/a	n/a
15	POLR2A	chr6:33662113-33666054	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:33664826-33665094	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr6:33664629-33665144	HepG2	liver:	n/a	n/a
18	MAFK	chr6:33664762-33665073	IMR90	lung:	n/a	n/a
19	POLR2A	chr6:33664664-33665260	U87	brain:	n/a	n/a
20	POLR2A	chr6:33664317-33665042	K562	blood:	n/a	n/a
21	NFIC	chr6:33664754-33665517	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr6:33664319-33665499	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr6:33664558-33665339	ECC-1	luminal epithelium:	n/a	n/a
24	NFIC	chr6:33664630-33665340	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr6:33664606-33665482	PFSK-1	brain:	n/a	n/a
26	REST	chr6:33664690-33665343	PFSK-1	brain:	n/a	chr6:33664788-33664808 chr6:33664794-33664808
27	ZNF263	chr6:33664630-33665178	HEK293-T-REx	kidney:	n/a	n/a
28	POLR2A	chr6:33663652-33665062	K562	blood:	n/a	n/a
29	POLR2A	chr6:33664663-33665043	U87	brain:	n/a	n/a
30	POLR2A	chr6:33662019-33665616	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr6:33657437-33666414	Hela-S3	cervix:	n/a	n/a
32	MAFK	chr6:33664786-33665034	HepG2	liver:	n/a	n/a
33	FOS	chr6:33664776-33665106	MCF10A-Er-Src	breast:	n/a	chr6:33664929-33664939 chr6:33664929-33664939 chr6:33664929-33664939
34	EP300	chr6:33664757-33665504	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr6:33664396-33665437	Hela-S3	cervix:	n/a	n/a
36	PML	chr6:33664978-33665621	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:33664995-33665257	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMC3	chr6:33664956-33665094	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr6:33658911-33667009	K562	blood:	n/a	n/a
40	CTCF	chr6:33664920-33665070	BE2_C	brain:	n/a	n/a
41	POLR2A	chr6:33664350-33665081	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:33664006-33665410	PANC-1	pancreas:	n/a	n/a
43	NFIC	chr6:33664681-33665262	SK-N-SH	brain:	n/a	n/a
44	MYC	chr6:33664883-33665067	HUVEC	blood vessel:	n/a	n/a
45	TCF12	chr6:33664857-33665279	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr6:33664744-33665321	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr6:33664630-33665710	HUVEC	blood vessel:	n/a	n/a
48	CHD2	chr6:33664975-33665094	Hela-S3	cervix:	n/a	n/a
49	FOS	chr6:33664692-33665332	HUVEC	blood vessel:	n/a	chr6:33664929-33664939 chr6:33664929-33664939 chr6:33665233-33665244 chr6:33664929-33664939
50	POLR2A	chr6:33657421-33665985	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
2	chr6:33588962..33590940-chr6:33663858..33665363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269490	TF binding region
MIR3934	TF binding region
ENSG00000096433	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	0.84[CEU][hapmap]
rs10947436	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs12110852	1.00[YRI][hapmap]
rs1536501	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1998949	1.00[JPT][hapmap]
rs2182659	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2395401	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2395448	1.00[JPT][hapmap]
rs2967	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4711350	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs498114	0.90[GIH][hapmap];1.00[JPT][hapmap]
rs530614	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs549652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597386	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs597723	0.83[ASN][1000 genomes]
rs602399	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs608971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623813	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs652049	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs654682	1.00[JPT][hapmap]
rs680608	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs684119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688209	0.84[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs751727	1.00[JPT][hapmap]
rs764753	1.00[JPT][hapmap]
rs943463	1.00[JPT][hapmap]
rs943464	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs943472	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs9461905	1.00[JPT][hapmap]
rs9469542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs658087	ITPR3	cis	multi-tissue	Pritchard
rs658087	UHRF1BP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
10	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
12	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr6:33659200-33665200	Genic enhancers	HMEC	breast
15	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
16	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:33659200-33666600	Enhancers	Right Atrium	heart
18	chr6:33659400-33666400	Genic enhancers	Fetal Thymus	thymus
19	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:33659600-33665600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:33659600-33666400	Enhancers	Primary hematopoietic stem cells	blood
22	chr6:33659600-33667000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:33659800-33665600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:33659800-33666000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr6:33659800-33666600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:33659800-33666600	Genic enhancers	Fetal Stomach	stomach
27	chr6:33660000-33666200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:33660200-33665600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:33660200-33667200	Genic enhancers	Lung	lung
30	chr6:33660200-33667800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:33660200-33669400	Strong transcription	HepG2	liver
32	chr6:33660400-33665600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:33660400-33665800	Enhancers	HUVEC	blood vessel
34	chr6:33660400-33666600	Genic enhancers	Thymus	Thymus
35	chr6:33660600-33666200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:33660800-33665400	Enhancers	Fetal Brain Male	brain
37	chr6:33661000-33665200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr6:33661200-33665200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:33661200-33665400	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr6:33661400-33669200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:33661600-33665400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:33661600-33665400	Genic enhancers	Gastric	stomach
43	chr6:33661600-33666200	Genic enhancers	Esophagus	oesophagus
44	chr6:33661600-33668600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr6:33661600-33668800	Genic enhancers	NHEK	skin
46	chr6:33661800-33665200	Enhancers	Brain Hippocampus Middle	brain
47	chr6:33661800-33665600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:33661800-33667200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:33661800-33675800	Weak transcription	Ovary	ovary
50	chr6:33662200-33665200	Enhancers	Brain Inferior Temporal Lobe	brain

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