Variant report

Variant	rs908817
Chromosome Location	chr15:76639191-76639192
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	RFX5	chr15:76638767-76639381	Hela-S3	cervix:	n/a	n/a
2	GATA2	chr15:76638789-76639801	HUVEC	blood vessel:	n/a	chr15:76639306-76639318
3	TAF1	chr15:76638727-76639221	ECC-1	luminal epithelium:	n/a	n/a
4	MAZ	chr15:76638133-76639454	Hela-S3	cervix:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
5	POLR2A	chr15:76637890-76639218	HepG2	liver:	n/a	n/a
6	CTBP2	chr15:76637866-76639885	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr15:76638899-76639289	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:76638078-76639268	Hela-S3	cervix:	n/a	n/a
9	MAX	chr15:76637983-76639383	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
10	POLR2A	chr15:76638868-76639245	HCT-116	colon:	n/a	n/a
11	MAX	chr15:76638134-76639329	Hela-S3	cervix:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
12	SMARCB1	chr15:76638041-76639719	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:76638941-76639212	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr15:76638078-76639374	Hela-S3	cervix:	n/a	n/a
15	MAX	chr15:76637967-76639337	H1-hESC	embryonic stem cell:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
16	EP300	chr15:76639187-76639395	Hela-S3	cervix:	n/a	n/a
17	SUZ12	chr15:76637988-76639646	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr15:76637887-76639835	H1-hESC	embryonic stem cell:	n/a	chr15:76639401-76639411 chr15:76638642-76638652 chr15:76639499-76639509 chr15:76638549-76638561 chr15:76639525-76639535
19	RAD21	chr15:76638801-76639208	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZBTB7A	chr15:76638028-76639213	ECC-1	luminal epithelium:	n/a	n/a
21	YY1	chr15:76637915-76639211	H1-hESC	embryonic stem cell:	n/a	chr15:76638648-76638659 chr15:76638852-76638863 chr15:76638835-76638844
22	MAX	chr15:76638885-76639232	ECC-1	luminal epithelium:	n/a	chr15:76639091-76639098
23	SUZ12	chr15:76637608-76640565	NT2-D1	testis:	n/a	n/a
24	GABPA	chr15:76638886-76639234	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:76638224-76639363	SK-N-MC	brain:	n/a	n/a
26	SMC3	chr15:76637945-76639327	Hela-S3	cervix:	n/a	chr15:76638223-76638233 chr15:76638171-76638179
27	KAP1	chr15:76637565-76639301	HEK293	kidney:	n/a	n/a
28	RCOR1	chr15:76638152-76639378	Hela-S3	cervix:	n/a	n/a
29	JUND	chr15:76639112-76639435	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr15:76637951-76639283	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
31	FOS	chr15:76639183-76639452	HUVEC	blood vessel:	n/a	n/a
32	GTF2F1	chr15:76639159-76639358	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:76638023-76639219	ECC-1	luminal epithelium:	n/a	n/a
34	ZNF263	chr15:76637630-76639781	HEK293-T-REx	kidney:	n/a	chr15:76639511-76639520 chr15:76639178-76639187
35	ZBTB7A	chr15:76638384-76639255	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr15:76639142-76639418	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr15:76638000-76639384	Hela-S3	cervix:	n/a	n/a
38	SIN3A	chr15:76638119-76639362	H1-hESC	embryonic stem cell:	n/a	chr15:76638617-76638630
39	MYC	chr15:76639001-76639372	H1-hESC	embryonic stem cell:	n/a	chr15:76639091-76639098
40	POLR2A	chr15:76639007-76639328	K562	blood:	n/a	n/a
41	GATA3	chr15:76639017-76639549	MCF-7	breast:	n/a	chr15:76639306-76639318

No.	Distal block	Cell Line	Cell type
1	chr15:76628671..76632944-chr15:76633969..76642252,10	MCF-7	breast:
2	chr15:76625840..76631025-chr15:76637216..76641688,7	MCF-7	breast:
3	chr15:76637265..76640642-chr15:76644223..76647135,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259514	TF binding region
ENSG00000140386	Chromatin interaction
ENSG00000159556	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11072591	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072597	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11072598	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11629888	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632222	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634019	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11635463	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11637490	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11638767	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855999	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11856717	0.87[CHB][hapmap]
rs11857015	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857327	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12591100	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12900179	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903874	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12906143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909656	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157783	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1607015	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1607017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs2003344	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2048856	0.82[ASN][1000 genomes]
rs2280306	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2436994	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2454450	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2454454	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2459361	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461870	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2461871	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461872	0.90[CHB][hapmap]
rs2468130	0.80[ASN][1000 genomes]
rs2468131	0.82[ASN][1000 genomes]
rs2469249	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs283789	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs283793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs283795	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2957614	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765115	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs437131	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs4886488	0.82[JPT][hapmap]
rs4886493	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886495	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886795	0.83[AMR][1000 genomes]
rs4886798	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4886805	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56246286	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62028380	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62028406	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62028423	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62028434	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71405204	0.83[AMR][1000 genomes]
rs744336	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8029283	0.88[CEU][hapmap];0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525769	chr15:76632487-76661925	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs908817	SCAPER	cis	lymphoblastoid	seeQTL
rs908817	SCAPER	cis	Adipose Subcutaneous	GTEx
rs908817	SCAPER	cis	Thyroid	GTEx
rs908817	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs908817	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs908817	SCAPER	cis	lung	GTEx
rs908817	SCAPER	cis	Nerve Tibial	GTEx
rs908817	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs908817	SCAPER	cis	Artery Tibial	GTEx
rs908817	NRG4	cis	parietal	SCAN
rs908817	SCAPER	cis	Esophagus Mucosa	GTEx
rs908817	SCAPER	cis	Whole Blood	GTEx
rs908817	SCAPER	cis	cerebellum	SCAN
rs908817	ISL2	cis	Whole Blood	GTEx
rs908817	SCAPER	cis	parietal	SCAN
rs908817	SCAPER	cis	Esophagus Muscularis	GTEx
rs908817	ISL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76630200-76641800	Weak transcription	A549	lung
2	chr15:76636400-76640200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:76637200-76640000	Weak transcription	K562	blood
4	chr15:76637800-76640200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:76638000-76639200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
6	chr15:76638000-76639400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:76638000-76639400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
8	chr15:76638000-76639400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
9	chr15:76638000-76639600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
10	chr15:76638000-76639600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
11	chr15:76638000-76639600	Flanking Bivalent TSS/Enh	NHEK	skin
12	chr15:76638000-76639800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:76638000-76639800	Enhancers	Spleen	Spleen
14	chr15:76638000-76640000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr15:76638000-76640000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr15:76638000-76640000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:76638000-76640400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr15:76638200-76639200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr15:76638200-76639200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:76638200-76639200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:76638200-76639200	Flanking Active TSS	Right Ventricle	heart
22	chr15:76638200-76639400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
23	chr15:76638200-76639600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
24	chr15:76638200-76639600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
25	chr15:76638200-76639600	Flanking Bivalent TSS/Enh	Placenta	Placenta
26	chr15:76638200-76639600	Active TSS	Hela-S3	cervix
27	chr15:76638200-76639800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:76638200-76639800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:76638200-76639800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:76638200-76640000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:76638200-76640000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr15:76638200-76640000	Bivalent Enhancer	Fetal Heart	heart
33	chr15:76638200-76640000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
34	chr15:76638200-76640200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr15:76638200-76640200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:76638400-76639200	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:76638400-76639200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr15:76638400-76639200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
39	chr15:76638400-76639200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr15:76638400-76639200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:76638400-76639200	Flanking Bivalent TSS/Enh	Liver	Liver
42	chr15:76638400-76639200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr15:76638400-76639200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
44	chr15:76638400-76639400	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:76638400-76639400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr15:76638400-76639400	Active TSS	HepG2	liver
47	chr15:76638400-76639600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
50	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood

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