Variant report

Variant	rs1801321
Chromosome Location	chr15:40987565-40987566
allele	G/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	POLR2A	chr15:40986626-40987656	HCT-116	colon:	n/a	n/a
2	MAX	chr15:40986680-40987917	K562	blood:	n/a	n/a
3	POLR2A	chr15:40986562-40987833	K562	blood:	n/a	n/a
4	POLR2A	chr15:40986625-40987633	HCT-116	colon:	n/a	n/a
5	POLR2A	chr15:40986643-40987577	U87	brain:	n/a	n/a
6	SP1	chr15:40986567-40987609	GM12878	blood:	n/a	chr15:40987075-40987089 chr15:40987313-40987322 chr15:40987314-40987323
7	BHLHE40	chr15:40986587-40987915	K562	blood:	n/a	chr15:40987770-40987786 chr15:40987390-40987406
8	SIN3AK20	chr15:40987026-40987860	PANC-1	pancreas:	n/a	n/a
9	EP300	chr15:40986846-40987745	K562	blood:	n/a	n/a
10	POLR2A	chr15:40987022-40987566	A549	lung:	n/a	n/a
11	POLR2A	chr15:40986569-40988010	HL-60	blood:	n/a	n/a
12	POLR2A	chr15:40986676-40987967	K562	blood:	n/a	n/a
13	POLR2A	chr15:40986697-40987864	K562	blood:	n/a	n/a
14	ETS1	chr15:40986746-40987864	K562	blood:	n/a	chr15:40987033-40987044
15	POLR2A	chr15:40986683-40987723	HUVEC	blood vessel:	n/a	n/a
16	TBL1XR1	chr15:40986709-40987570	K562	blood:	n/a	n/a
17	E2F4	chr15:40986644-40988122	Hela-S3	cervix:	n/a	chr15:40987362-40987373 chr15:40987362-40987370 chr15:40987363-40987370 chr15:40987364-40987375 chr15:40987313-40987322 chr15:40987363-40987371 chr15:40987587-40987597 chr15:40987363-40987374 chr15:40987363-40987371 chr15:40987362-40987372
18	ETS1	chr15:40986168-40987937	GM12878	blood:	n/a	chr15:40987033-40987044
19	TEAD4	chr15:40986470-40987606	K562	blood:	n/a	n/a
20	POLR2A	chr15:40986315-40987930	GM19193	blood:	n/a	n/a
21	MAX	chr15:40986695-40988049	Hela-S3	cervix:	n/a	chr15:40988005-40988014
22	MTA3	chr15:40985866-40988075	GM12878	blood:	n/a	n/a
23	NR2F2	chr15:40987116-40987657	K562	blood:	n/a	n/a
24	SIN3AK20	chr15:40986698-40987803	PFSK-1	brain:	n/a	n/a
25	PML	chr15:40986864-40987705	K562	blood:	n/a	n/a
26	YY1	chr15:40986571-40987584	GM12878	blood:	n/a	n/a
27	MAX	chr15:40986195-40988024	NB4	blood:	n/a	chr15:40988005-40988014
28	ZNF143	chr15:40986560-40987917	Hela-S3	cervix:	n/a	chr15:40987032-40987042
29	IRF1	chr15:40986629-40987608	K562	blood:	n/a	chr15:40987312-40987326
30	RELA	chr15:40986252-40988005	GM15510	blood:	n/a	n/a
31	POLR2A	chr15:40986747-40987740	ProgFib	skin:	n/a	n/a
32	POLR2A	chr15:40986670-40987579	GM12878	blood:	n/a	n/a
33	MAX	chr15:40986773-40987692	A549	lung:	n/a	n/a
34	BCLAF1	chr15:40986314-40987827	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:40986453-40987846	PFSK-1	brain:	n/a	n/a
36	TCF12	chr15:40986628-40987808	GM12878	blood:	n/a	chr15:40987590-40987600
37	SIN3AK20	chr15:40986874-40988169	MCF-7	breast:	n/a	n/a
38	CREB1	chr15:40987117-40987786	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr15:40986401-40988210	Hela-S3	cervix:	n/a	n/a
40	CHD2	chr15:40986588-40987935	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr15:40986191-40987836	NB4	blood:	n/a	n/a
42	ELF1	chr15:40986648-40988004	GM12878	blood:	n/a	n/a
43	BCLAF1	chr15:40986513-40987617	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:40986497-40987772	GM12892	blood:	n/a	n/a
45	MAX	chr15:40986650-40988017	A549	lung:	n/a	chr15:40988005-40988014
46	BHLHE40	chr15:40986451-40987790	GM12878	blood:	n/a	chr15:40987770-40987786 chr15:40987390-40987406
47	HMGN3	chr15:40986825-40987906	K562	blood:	n/a	n/a
48	ETS1	chr15:40986613-40987748	K562	blood:	n/a	chr15:40987033-40987044
49	TAF1	chr15:40987168-40987774	HepG2	liver:	n/a	n/a
50	HCFC1	chr15:40986562-40987634	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40985078..40988247-chr15:41185737..41188201,3	K562	blood:
2	chr15:40986013..40988355-chr15:41045826..41048654,2	MCF-7	breast:
3	chr15:40885583..40887494-chr15:40985320..40988301,2	K562	blood:
4	chr15:40985800..40990095-chr15:41055400..41057901,4	K562	blood:
5	chr15:40987298..40988058-chr17:62502299..62503222,2	Hela-S3	cervix:
6	chr15:40987359..40990886-chr15:41044779..41048321,5	K562	blood:
7	chr15:40987273..40988882-chr15:41061961..41063775,2	K562	blood:
8	chr15:40986558..40989601-chr15:40990368..40993764,9	K562	blood:
9	chr15:40985310..40988262-chr15:41045857..41048554,2	MCF-7	breast:
10	chr15:40986884..40987798-chr15:41575787..41576375,2	Hela-S3	cervix:
11	chr15:40986980..40987882-chr6:30584915..30585502,2	Hela-S3	cervix:
12	chr15:40860821..40863087-chr15:40987318..40989233,3	K562	blood:
13	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:
14	chr15:40986981..40987821-chr3:44379041..44379997,2	Hela-S3	cervix:
15	chr15:40986478..40988882-chr15:41036813..41039846,3	K562	blood:

Variant related genes	Relation type
RAD51-AS1	TF binding region
RAD51	TF binding region
ENSG00000166133	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000179152	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000247556	Chromatin interaction
ENSG00000137812	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10152546	0.92[CEU][hapmap]
rs1044474	0.89[CEU][hapmap]
rs10518697	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1058734	0.93[CEU][hapmap]
rs11070283	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs12148915	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12385982	0.80[AMR][1000 genomes]
rs12442560	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12591044	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592524	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903817	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12907442	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12908316	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12913739	0.93[CEU][hapmap]
rs12915171	0.92[CEU][hapmap]
rs12915636	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17673703	0.92[CEU][hapmap]
rs17674454	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs17747423	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17747633	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2619682	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28866515	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28891195	0.85[AMR][1000 genomes]
rs34305357	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34739056	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35127391	0.83[AMR][1000 genomes]
rs35684277	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4923880	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4924486	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4924492	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924496	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924498	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924502	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5030789	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56409425	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59244061	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492964	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71471880	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7165509	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7175747	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7175905	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176245	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176590	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177265	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7180135	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182499	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8029530	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036891	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037180	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8038122	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8042386	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs957603	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9920676	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1801321	CCDC32	cis	normal skin	skin_eQTL
rs1801321	C15orf57	cis	Esophagus Muscularis	GTEx
rs1801321	C15orf57	cis	Muscle Skeletal	GTEx
rs1801321	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs1801321	C15orf57	cis	Nerve Tibial	GTEx
rs1801321	RP11-111A22.1	cis	Artery Tibial	GTEx
rs1801321	C15orf57	cis	Heart Left Ventricle	GTEx
rs1801321	RAD51	cis	multi-tissue	Pritchard
rs1801321	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs1801321	C15orf57	cis	lung	GTEx
rs1801321	C15orf57	cis	Esophagus Mucosa	GTEx
rs1801321	C15orf57	cis	Artery Aorta	GTEx
rs1801321	C15orf57	cis	Stomach	GTEx
rs1801321	C15orf57	cis	Artery Tibial	GTEx
rs1801321	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs1801321	C15orf57	cis	Adipose Subcutaneous	GTEx
rs1801321	RP11-111A22.1	cis	lung	GTEx
rs1801321	CCDC32	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40986000-40987800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr15:40986000-40988400	Active TSS	GM12878-XiMat	blood
3	chr15:40986000-40988400	Active TSS	NHDF-Ad	bronchial
4	chr15:40986000-40988600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:40986000-40988600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:40986000-40988600	Active TSS	NH-A	brain
7	chr15:40986000-40988800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:40986000-40989000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr15:40986000-40989200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:40986200-40988000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:40986200-40988200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:40986200-40988200	Bivalent/Poised TSS	HepG2	liver
13	chr15:40986200-40988400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr15:40986200-40988400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:40986200-40988600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr15:40986200-40988600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:40986200-40988800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr15:40986200-40988800	Active TSS	Fetal Kidney	kidney
19	chr15:40986200-40989000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:40986200-40989000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:40986200-40989000	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr15:40986200-40989200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:40986400-40987600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr15:40986400-40987600	Active TSS	Lung	lung
25	chr15:40986400-40987800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:40986400-40987800	Active TSS	Ovary	ovary
27	chr15:40986400-40988000	Active TSS	Aorta	Aorta
28	chr15:40986400-40988000	Active TSS	Left Ventricle	heart
29	chr15:40986400-40988000	Active TSS	Pancreas	Pancrea
30	chr15:40986400-40988000	Active TSS	Psoas Muscle	Psoas
31	chr15:40986400-40988000	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr15:40986400-40988200	Active TSS	Esophagus	oesophagus
33	chr15:40986400-40988200	Active TSS	Small Intestine	intestine
34	chr15:40986400-40988200	Active TSS	HSMMtube	muscle
35	chr15:40986400-40988400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:40986400-40988400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:40986400-40988400	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr15:40986400-40988400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:40986400-40988400	Active TSS	Fetal Intestine Large	intestine
40	chr15:40986400-40988400	Active TSS	Dnd41	blood
41	chr15:40986400-40988400	Active TSS	NHEK	skin
42	chr15:40986400-40988600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:40986400-40988600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:40986400-40988600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:40986400-40988600	Active TSS	A549	lung
46	chr15:40986400-40988800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:40986400-40988800	Active TSS	HSMM	muscle
48	chr15:40986400-40988800	Active TSS	NHLF	lung
49	chr15:40986400-40989200	Active TSS	K562	blood
50	chr15:40986600-40987600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links