Variant report

Variant	rs13239077
Chromosome Location	chr7:5085005-5085006
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	POLR2A	chr7:5084829-5086642	H1-hESC	embryonic stem cell:	n/a	n/a
2	CBX3	chr7:5084916-5085678	K562	blood:	n/a	n/a
3	POLR2A	chr7:5084957-5086650	GM12891	blood:	n/a	n/a
4	HEY1	chr7:5084991-5085708	K562	blood:	n/a	chr7:5085469-5085484
5	RXRA	chr7:5084845-5085871	HepG2	liver:	n/a	chr7:5085722-5085742 chr7:5085045-5085054
6	POLR2A	chr7:5085000-5085930	U87	brain:	n/a	n/a
7	POLR2A	chr7:5084947-5085751	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:5084993-5085707	H1-hESC	embryonic stem cell:	n/a	n/a
9	CBX3	chr7:5084932-5085666	K562	blood:	n/a	n/a
10	POLR2A	chr7:5084959-5086207	PFSK-1	brain:	n/a	n/a
11	NFIC	chr7:5084968-5085674	GM12878	blood:	n/a	n/a
12	SP1	chr7:5084946-5085687	GM12878	blood:	n/a	n/a
13	POU2F2	chr7:5084720-5085722	GM12891	blood:	n/a	chr7:5085615-5085627
14	POLR2A	chr7:5085004-5085884	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr7:5084940-5086626	GM12891	blood:	n/a	n/a
16	POLR2A	chr7:5084932-5086518	SK-N-MC	brain:	n/a	n/a
17	NR2F2	chr7:5084974-5085718	K562	blood:	n/a	n/a
18	POLR2A	chr7:5084942-5086642	GM12891	blood:	n/a	n/a
19	POLR2A	chr7:5085000-5086101	U87	brain:	n/a	n/a
20	MTA3	chr7:5084997-5085678	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:5084870-5087186	GM12878	blood:	n/a	n/a
22	TAF1	chr7:5084913-5086164	H1-hESC	embryonic stem cell:	n/a	n/a
23	PAX5	chr7:5084955-5085730	GM12878	blood:	n/a	chr7:5085045-5085054
24	POU2F2	chr7:5084931-5085788	GM12878	blood:	n/a	chr7:5085615-5085627 chr7:5085737-5085749
25	POLR2A	chr7:5084969-5085762	U87	brain:	n/a	n/a
26	PML	chr7:5084939-5085816	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:5084953-5085300	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr7:5084939-5087842	GM12878	blood:	n/a	n/a
29	HEY1	chr7:5084982-5086627	K562	blood:	n/a	chr7:5086070-5086079 chr7:5085886-5085901 chr7:5085469-5085484 chr7:5085973-5085988 chr7:5085700-5085715
30	HEY1	chr7:5084923-5086524	HepG2	liver:	n/a	chr7:5086070-5086079 chr7:5085886-5085901 chr7:5085469-5085484 chr7:5085973-5085988 chr7:5085700-5085715

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:4920954..4923771-chr7:5084405..5086180,2	K562	blood:

Variant related genes	Relation type
RBAK	TF binding region
RBAK-RBAKDN	TF binding region
ENSG00000157927	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10085591	0.86[ASN][1000 genomes]
rs10215776	0.86[ASN][1000 genomes]
rs10226147	0.82[ASN][1000 genomes]
rs10228158	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10229468	0.82[ASN][1000 genomes]
rs10240940	0.85[ASN][1000 genomes]
rs10245090	0.86[ASN][1000 genomes]
rs10245738	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10246340	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10272726	0.83[ASN][1000 genomes]
rs10275581	0.86[ASN][1000 genomes]
rs10281718	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10951759	0.86[ASN][1000 genomes]
rs10951760	0.86[ASN][1000 genomes]
rs10951761	0.86[ASN][1000 genomes]
rs10951764	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1127434	0.81[ASN][1000 genomes]
rs11971044	0.86[ASN][1000 genomes]
rs11971647	0.85[ASN][1000 genomes]
rs11972914	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11976691	0.86[EUR][1000 genomes]
rs11976846	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11978674	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11984402	0.89[AMR][1000 genomes]
rs12234314	0.91[ASN][1000 genomes]
rs12334144	0.84[ASN][1000 genomes]
rs12669641	0.84[ASN][1000 genomes]
rs12670409	0.85[ASN][1000 genomes]
rs12672515	0.82[ASN][1000 genomes]
rs13228234	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13229764	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13236130	0.86[ASN][1000 genomes]
rs13240149	0.85[ASN][1000 genomes]
rs13242424	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13243386	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28449930	0.85[ASN][1000 genomes]
rs28564852	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28785867	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28806564	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28817909	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28872635	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34150359	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34483734	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34603194	0.82[ASN][1000 genomes]
rs34974055	0.88[ASN][1000 genomes]
rs35013001	0.82[ASN][1000 genomes]
rs35145208	0.87[AMR][1000 genomes]
rs35610193	0.88[ASN][1000 genomes]
rs35747848	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35780021	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35875647	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs36039016	0.84[ASN][1000 genomes]
rs4257923	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4268029	0.82[ASN][1000 genomes]
rs4283955	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4338005	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4380823	0.81[ASN][1000 genomes]
rs4397302	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4403324	0.84[ASN][1000 genomes]
rs4431493	0.88[ASN][1000 genomes]
rs4476909	0.88[ASN][1000 genomes]
rs4523153	0.84[ASN][1000 genomes]
rs4573157	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4585633	0.84[ASN][1000 genomes]
rs4590348	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4720472	0.81[ASN][1000 genomes]
rs60579433	0.83[ASN][1000 genomes]
rs61116960	0.85[ASN][1000 genomes]
rs61296609	0.85[ASN][1000 genomes]
rs62444301	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62444313	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62444315	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6463220	0.82[ASN][1000 genomes]
rs6463225	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6463228	0.89[ASN][1000 genomes]
rs6942686	0.85[ASN][1000 genomes]
rs6951140	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6958077	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6959877	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6960279	0.82[ASN][1000 genomes]
rs6960304	0.82[ASN][1000 genomes]
rs6965179	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6971154	0.86[ASN][1000 genomes]
rs6971796	0.85[EUR][1000 genomes]
rs6973878	0.84[ASN][1000 genomes]
rs7457066	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7778444	0.84[ASN][1000 genomes]
rs7779828	0.82[ASN][1000 genomes]
rs7780922	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7781429	0.96[ASN][1000 genomes]
rs7782190	0.81[ASN][1000 genomes]
rs7786822	0.82[ASN][1000 genomes]
rs7787140	0.82[ASN][1000 genomes]
rs7794683	0.84[ASN][1000 genomes]
rs7800799	0.83[ASN][1000 genomes]
rs7802223	0.81[ASN][1000 genomes]
rs9769480	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9769483	0.87[ASN][1000 genomes]
rs9771477	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9886313	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
9	nsv1019120	chr7:4929653-5138409	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv917078	chr7:4962123-5151633	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv966749	chr7:5036761-5098568	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1029430	chr7:5053887-5223583	Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv1034446	chr7:5066181-5108770	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv1025644	chr7:5066181-5114089	Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1032880	chr7:5066181-5205932	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
16	nsv1030384	chr7:5066181-5210555	Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
17	nsv966924	chr7:5070042-5086142	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5051200-5085200	Weak transcription	Aorta	Aorta
2	chr7:5077800-5085200	Weak transcription	Lung	lung
3	chr7:5081400-5085200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:5081400-5085400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:5083000-5085400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:5084400-5087200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:5084600-5085200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr7:5084600-5086400	Active TSS	Brain Substantia Nigra	brain
9	chr7:5084600-5087000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr7:5084800-5085200	Enhancers	Primary B cells from peripheral blood	blood
11	chr7:5084800-5085200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:5084800-5085200	Enhancers	Small Intestine	intestine
13	chr7:5084800-5086000	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr7:5084800-5086800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:5084800-5086800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:5084800-5086800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr7:5084800-5086800	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr7:5085000-5085200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:5085000-5085200	Enhancers	Primary hematopoietic stem cells	blood
20	chr7:5085000-5085200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:5085000-5085200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr7:5085000-5085200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr7:5085000-5085200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:5085000-5085200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr7:5085000-5085200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr7:5085000-5085200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr7:5085000-5085200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:5085000-5085200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:5085000-5085200	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr7:5085000-5085200	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr7:5085000-5085200	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr7:5085000-5085200	Enhancers	Fetal Brain Male	brain
33	chr7:5085000-5085200	Enhancers	Fetal Muscle Leg	muscle
34	chr7:5085000-5085200	Enhancers	Stomach Mucosa	stomach
35	chr7:5085000-5085200	Enhancers	HepG2	liver
36	chr7:5085000-5085200	Enhancers	HUVEC	blood vessel
37	chr7:5085000-5085200	Enhancers	NH-A	brain
38	chr7:5085000-5085400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:5085000-5085400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:5085000-5085400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:5085000-5085400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr7:5085000-5085400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr7:5085000-5085400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:5085000-5085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:5085000-5085400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr7:5085000-5085400	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr7:5085000-5085400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr7:5085000-5085400	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr7:5085000-5085400	Flanking Active TSS	Fetal Stomach	stomach
50	chr7:5085000-5085400	Flanking Active TSS	Fetal Thymus	thymus

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