Variant report

Variant	rs58677957
Chromosome Location	chr15:39881379-39881380
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	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	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
7	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr15:39877301-39881618	PBDE	blood:	n/a	n/a
9	POLR2A	chr15:39876821-39881379	HepG2	liver:	n/a	n/a
10	POLR2A	chr15:39881336-39881564	A549	lung:	n/a	n/a
11	POLR2A	chr15:39880439-39881557	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	POLR2A	chr15:39877424-39887319	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr15:39879988-39881622	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:39877387-39882925	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:39879988-39881485	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr15:39876934-39882780	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39877214..39880046-chr15:39880170..39882635,2	K562	blood:

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

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10083552	1.00[EUR][1000 genomes]
rs1551946	1.00[ASN][1000 genomes]
rs16969232	1.00[ASN][1000 genomes]
rs16969234	1.00[ASN][1000 genomes]
rs16969236	1.00[ASN][1000 genomes]
rs16969237	1.00[ASN][1000 genomes]
rs16969251	1.00[ASN][1000 genomes]
rs16969254	1.00[ASN][1000 genomes]
rs16969307	1.00[EUR][1000 genomes]
rs16969364	1.00[EUR][1000 genomes]
rs16969365	1.00[EUR][1000 genomes]
rs16969384	1.00[EUR][1000 genomes]
rs16969484	1.00[EUR][1000 genomes]
rs16969573	1.00[EUR][1000 genomes]
rs1876850	1.00[ASN][1000 genomes]
rs1876851	1.00[ASN][1000 genomes]
rs1961097	1.00[ASN][1000 genomes]
rs28390974	1.00[ASN][1000 genomes]
rs28433877	1.00[ASN][1000 genomes]
rs28605448	1.00[ASN][1000 genomes]
rs41376748	1.00[EUR][1000 genomes]
rs41406047	1.00[EUR][1000 genomes]
rs41515347	1.00[EUR][1000 genomes]
rs41519250	1.00[ASN][1000 genomes]
rs57247690	1.00[ASN][1000 genomes]
rs57383264	1.00[ASN][1000 genomes]
rs58042874	1.00[ASN][1000 genomes]
rs58319120	1.00[ASN][1000 genomes]
rs58716252	1.00[EUR][1000 genomes]
rs58789628	1.00[ASN][1000 genomes]
rs58886304	1.00[ASN][1000 genomes]
rs59146042	1.00[EUR][1000 genomes]
rs59648752	1.00[ASN][1000 genomes]
rs61040173	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61201811	1.00[ASN][1000 genomes]
rs6492901	1.00[ASN][1000 genomes]
rs6492903	1.00[ASN][1000 genomes]
rs6492904	1.00[ASN][1000 genomes]
rs7162555	1.00[ASN][1000 genomes]
rs7163020	1.00[EUR][1000 genomes]
rs7163169	1.00[ASN][1000 genomes]
rs7166970	1.00[ASN][1000 genomes]
rs7167206	1.00[ASN][1000 genomes]
rs7168679	1.00[ASN][1000 genomes]
rs7168836	1.00[ASN][1000 genomes]
rs7172057	1.00[EUR][1000 genomes]
rs7175706	1.00[ASN][1000 genomes]
rs7183198	1.00[ASN][1000 genomes]
rs73385184	1.00[ASN][1000 genomes]
rs73385188	1.00[ASN][1000 genomes]
rs73385190	1.00[ASN][1000 genomes]
rs73387008	1.00[ASN][1000 genomes]
rs73387053	1.00[ASN][1000 genomes]
rs73387054	1.00[ASN][1000 genomes]
rs73387057	1.00[ASN][1000 genomes]
rs73387060	1.00[ASN][1000 genomes]
rs73387062	1.00[ASN][1000 genomes]
rs73387065	1.00[ASN][1000 genomes]
rs73387069	1.00[ASN][1000 genomes]
rs73389089	1.00[ASN][1000 genomes]
rs73389092	1.00[ASN][1000 genomes]
rs73389096	1.00[ASN][1000 genomes]
rs73391204	1.00[ASN][1000 genomes]
rs73391206	1.00[ASN][1000 genomes]
rs73391226	1.00[ASN][1000 genomes]
rs73391234	1.00[ASN][1000 genomes]
rs74008705	1.00[EUR][1000 genomes]
rs8023525	1.00[EUR][1000 genomes]
rs8024038	1.00[ASN][1000 genomes]
rs8024502	1.00[ASN][1000 genomes]
rs8024606	1.00[ASN][1000 genomes]
rs8024670	1.00[ASN][1000 genomes]
rs8024886	1.00[ASN][1000 genomes]
rs8029417	1.00[EUR][1000 genomes]
rs8030643	1.00[EUR][1000 genomes]
rs8031289	1.00[EUR][1000 genomes]
rs8033803	1.00[EUR][1000 genomes]
rs8035627	1.00[EUR][1000 genomes]
rs8038776	1.00[ASN][1000 genomes]
rs8039379	1.00[ASN][1000 genomes]
rs8041420	1.00[ASN][1000 genomes]
rs8043342	1.00[EUR][1000 genomes]
rs878941	1.00[EUR][1000 genomes]
rs937955	1.00[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	chr15:39873400-39881600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:39873400-39884200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr15:39873400-39884200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
6	chr15:39873400-39886800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:39873600-39882200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
8	chr15:39873600-39882200	Transcr. at gene 5' and 3'	HSMM	muscle
9	chr15:39873600-39884000	Transcr. at gene 5' and 3'	HMEC	breast
10	chr15:39873600-39884000	Transcr. at gene 5' and 3'	Osteobl	bone
11	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
12	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
13	chr15:39875200-39887800	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:39875400-39881400	Genic enhancers	Liver	Liver
17	chr15:39875400-39886000	Weak transcription	Psoas Muscle	Psoas
18	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:39876000-39882200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:39876000-39886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:39876000-39886600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:39876000-39886800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:39876000-39888600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:39876200-39888200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:39876400-39886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:39876600-39882200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:39876600-39883400	Strong transcription	Pancreas	Pancrea
33	chr15:39876600-39886400	Strong transcription	Lung	lung
34	chr15:39876800-39882200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr15:39876800-39885200	Weak transcription	Small Intestine	intestine
36	chr15:39877000-39887600	Weak transcription	Brain Germinal Matrix	brain
37	chr15:39877200-39882600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr15:39877200-39886000	Strong transcription	A549	lung
39	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:39877400-39882200	Strong transcription	Fetal Intestine Small	intestine
41	chr15:39877800-39882200	Strong transcription	Gastric	stomach
42	chr15:39877800-39887200	Weak transcription	Fetal Thymus	thymus
43	chr15:39877800-39888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:39877800-39888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:39878000-39882200	Strong transcription	Colonic Mucosa	Colon
46	chr15:39878000-39882200	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:39878000-39888400	Strong transcription	Left Ventricle	heart
48	chr15:39878000-39890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:39878200-39886800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr15:39878200-39888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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