Variant report

Variant	rs1134485
Chromosome Location	chr15:39879981-39879982
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	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:39872374-39882964	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr15:39871542-39884619	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr15:39877373-39881604	A549	lung:	n/a	n/a
5	USF2	chr15:39879494-39882452	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr15:39879654-39881289	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
8	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr15:39877301-39881618	PBDE	blood:	n/a	n/a
10	POLR2A	chr15:39876821-39881379	HepG2	liver:	n/a	n/a
11	POLR2A	chr15:39879973-39880208	HepG2	liver:	n/a	n/a
12	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
13	POLR2A	chr15:39876842-39884440	MCF-7	breast:	n/a	n/a
14	POLR2A	chr15:39878113-39884419	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr15:39871578-39884189	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
20	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr15:39871703-39884436	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
23	FOXA1	chr15:39879922-39880183	T-47D	breast:	n/a	chr15:39880076-39880091
24	POLR2A	chr15:39877424-39887319	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr15:39877387-39882925	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:39876934-39882780	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39878404..39880564-chr15:40074822..40077432,2	MCF-7	breast:
2	chr15:39877214..39880046-chr15:39880170..39882635,2	K562	blood:

Variant related genes	Relation type
THBS1	TF binding region
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1004739	1.00[CEU][hapmap]
rs1004740	1.00[CEU][hapmap]
rs10152640	0.90[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs10520135	0.87[CEU][hapmap]
rs10520137	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs10520138	0.80[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs11070220	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070221	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070222	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070223	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070224	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070225	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1134486	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11630406	1.00[CEU][hapmap]
rs11631570	1.00[CEU][hapmap]
rs11632879	1.00[CEU][hapmap]
rs11633974	1.00[CEU][hapmap]
rs11635103	1.00[CEU][hapmap]
rs11638041	1.00[CEU][hapmap]
rs11638500	1.00[CEU][hapmap]
rs11852591	1.00[CEU][hapmap]
rs11852649	1.00[CEU][hapmap]
rs11854797	1.00[CEU][hapmap]
rs11856294	1.00[CEU][hapmap]
rs11856971	1.00[CEU][hapmap]
rs11857819	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11857927	1.00[CEU][hapmap]
rs12443011	0.80[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs12908846	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12912082	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1478604	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1478605	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs16969386	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16969395	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16969410	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16969445	1.00[CEU][hapmap]
rs16969459	1.00[CEU][hapmap]
rs16969460	1.00[CEU][hapmap]
rs16969475	1.00[CEU][hapmap]
rs16969478	1.00[CEU][hapmap];0.80[CHD][hapmap]
rs1876853	1.00[CEU][hapmap]
rs1904209	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169830	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2228261	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229364	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292305	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411313	1.00[CEU][hapmap]
rs2412409	1.00[CEU][hapmap]
rs2412413	1.00[CEU][hapmap]
rs2412415	1.00[CEU][hapmap]
rs2412417	1.00[CEU][hapmap]
rs2412419	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2412420	0.86[ASN][1000 genomes]
rs2412421	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2618162	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2618163	0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2664139	0.89[ASN][1000 genomes]
rs2664141	0.97[ASN][1000 genomes]
rs2898686	1.00[CEU][hapmap]
rs2898687	1.00[CEU][hapmap]
rs2898688	1.00[CEU][hapmap]
rs3743125	0.81[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784390	1.00[CEU][hapmap]
rs4349120	1.00[CEU][hapmap]
rs4476147	1.00[CEU][hapmap]
rs4547308	1.00[CEU][hapmap]
rs4583211	1.00[CEU][hapmap]
rs56938133	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67239630	0.86[ASN][1000 genomes]
rs7162070	1.00[CEU][hapmap]
rs7162781	1.00[CEU][hapmap]
rs7167184	1.00[CEU][hapmap]
rs7167366	0.85[ASN][1000 genomes]
rs7168755	1.00[CEU][hapmap]
rs7169478	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7169574	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7170682	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177324	0.88[ASN][1000 genomes]
rs7179293	0.80[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7183544	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs753598	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs753599	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8029602	1.00[CEU][hapmap]
rs8032035	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8034594	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs8036376	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036633	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8039035	0.83[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs884584	1.00[CEU][hapmap]
rs9302102	0.81[EUR][1000 genomes]
rs949646	0.80[CHB][hapmap];0.86[ASN][1000 genomes]
rs964424	0.90[ASN][1000 genomes]
rs970280	0.83[ASN][1000 genomes]
rs9806647	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39872600-39882400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:39872800-39881600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:39873400-39880800	Transcr. at gene 5' and 3'	NHLF	lung
4	chr15:39873400-39881600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:39873400-39884200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
6	chr15:39873400-39884200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
7	chr15:39873400-39886800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:39873600-39882200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
9	chr15:39873600-39882200	Transcr. at gene 5' and 3'	HSMM	muscle
10	chr15:39873600-39884000	Transcr. at gene 5' and 3'	HMEC	breast
11	chr15:39873600-39884000	Transcr. at gene 5' and 3'	Osteobl	bone
12	chr15:39874600-39880400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
13	chr15:39874600-39880400	Transcr. at gene 5' and 3'	HSMMtube	muscle
14	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
15	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
16	chr15:39875200-39880200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:39875200-39887800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:39875400-39881200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:39875400-39881400	Genic enhancers	Liver	Liver
22	chr15:39875400-39886000	Weak transcription	Psoas Muscle	Psoas
23	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:39875800-39880000	Genic enhancers	Fetal Heart	heart
27	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:39876000-39882200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:39876000-39886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:39876000-39886600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:39876000-39886800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:39876000-39888600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:39876200-39888200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:39876400-39886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:39876600-39880600	Genic enhancers	Ovary	ovary
38	chr15:39876600-39882200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:39876600-39883400	Strong transcription	Pancreas	Pancrea
40	chr15:39876600-39886400	Strong transcription	Lung	lung
41	chr15:39876800-39880200	Strong transcription	Fetal Intestine Large	intestine
42	chr15:39876800-39880800	Genic enhancers	Colon Smooth Muscle	Colon
43	chr15:39876800-39882200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr15:39876800-39885200	Weak transcription	Small Intestine	intestine
45	chr15:39877000-39887600	Weak transcription	Brain Germinal Matrix	brain
46	chr15:39877200-39880800	Genic enhancers	Fetal Stomach	stomach
47	chr15:39877200-39882600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr15:39877200-39886000	Strong transcription	A549	lung
49	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:39877400-39882200	Strong transcription	Fetal Intestine Small	intestine

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