Variant report

Variant	rs2575772
Chromosome Location	chr3:87040392-87040393
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	CREB1	chr3:87039716-87040721	A549	lung:	n/a	n/a
2	TEAD4	chr3:87040330-87040823	H1-hESC	embryonic stem cell:	n/a	n/a
3	CREB1	chr3:87040069-87040660	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF7L2	chr3:87039595-87040695	HCT-116	colon:	n/a	chr3:87039758-87039767
5	MAX	chr3:87040102-87040704	A549	lung:	n/a	chr3:87040369-87040379 chr3:87040357-87040367 chr3:87040621-87040632
6	TEAD4	chr3:87040316-87040786	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP4	chr3:87040373-87040733	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF1	chr3:87040019-87040635	A549	lung:	n/a	n/a
9	CTCF	chr3:87040380-87040530	NHDF-neo	bronchial:	n/a	n/a
10	E2F6	chr3:87039970-87040842	H1-hESC	embryonic stem cell:	n/a	chr3:87040356-87040365 chr3:87040160-87040170
11	HA-E2F1	chr3:87039577-87040690	Hela-S3	cervix:	n/a	chr3:87040356-87040365 chr3:87039732-87039741 chr3:87040160-87040170 chr3:87040129-87040140
12	SP1	chr3:87040000-87040719	H1-hESC	embryonic stem cell:	n/a	chr3:87040365-87040379 chr3:87040356-87040365 chr3:87040355-87040367 chr3:87040352-87040366 chr3:87040368-87040379 chr3:87040355-87040366
13	TAF1	chr3:87040370-87040627	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:87040380-87040530	HAc	cerebellar:	n/a	n/a
15	MAX	chr3:87039418-87040896	A549	lung:	n/a	chr3:87040369-87040379 chr3:87040357-87040367 chr3:87040621-87040632
16	RAD21	chr3:87040374-87041290	Hela-S3	cervix:	n/a	n/a
17	TCF12	chr3:87039927-87040824	A549	lung:	n/a	n/a
18	ZBTB7A	chr3:87039393-87040798	ECC-1	luminal epithelium:	n/a	n/a
19	CTCF	chr3:87040376-87040652	Fibrobl	skin:	n/a	n/a
20	TCF12	chr3:87039565-87040755	ECC-1	luminal epithelium:	n/a	chr3:87039593-87039603
21	RCOR1	chr3:87039141-87041114	Hela-S3	cervix:	n/a	n/a
22	EP300	chr3:87039540-87040764	H1-hESC	embryonic stem cell:	n/a	chr3:87040148-87040164
23	MAX	chr3:87039241-87040898	Hela-S3	cervix:	n/a	chr3:87040369-87040379 chr3:87040357-87040367 chr3:87040621-87040632
24	RAD21	chr3:87039389-87040892	IMR90	lung:	n/a	chr3:87039734-87039744 chr3:87039734-87039748
25	E2F6	chr3:87039436-87040904	H1-hESC	embryonic stem cell:	n/a	chr3:87040356-87040365 chr3:87039732-87039741 chr3:87040160-87040170
26	TBP	chr3:87038136-87041700	Hela-S3	cervix:	n/a	n/a
27	NFYA	chr3:87040369-87040615	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:87039814-87040914	U87	brain:	n/a	n/a
29	POLR2A	chr3:87034376-87041427	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr3:87039600-87040897	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr3:87040379-87040812	ECC-1	luminal epithelium:	n/a	n/a
32	JUND	chr3:87039559-87040693	H1-hESC	embryonic stem cell:	n/a	chr3:87040355-87040364 chr3:87039758-87039767
33	TAF1	chr3:87040388-87040723	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIN3A	chr3:87039346-87041055	H1-hESC	embryonic stem cell:	n/a	chr3:87040220-87040233
35	POLR2A	chr3:87039493-87040920	U87	brain:	n/a	n/a
36	CREB1	chr3:87039992-87040724	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr3:87040340-87040490	HRPEpiC	eye:	n/a	n/a
38	CTBP2	chr3:87039346-87040795	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:87039376-87040914	H1-hESC	embryonic stem cell:	n/a	n/a
40	SMC3	chr3:87038973-87040848	Hela-S3	cervix:	n/a	chr3:87040164-87040174 chr3:87039734-87039744 chr3:87040458-87040468
41	MAX	chr3:87039499-87040845	H1-hESC	embryonic stem cell:	n/a	chr3:87040369-87040379 chr3:87040357-87040367 chr3:87040621-87040632
42	POLR2A	chr3:87039571-87040810	A549	lung:	n/a	n/a
43	MAZ	chr3:87039396-87040850	IMR90	lung:	n/a	chr3:87040369-87040379 chr3:87040357-87040367 chr3:87040621-87040632
44	CTCF	chr3:87040380-87040530	HCFaa	heart:	n/a	n/a
45	TCF7L2	chr3:87039481-87040801	Hela-S3	cervix:	n/a	chr3:87039758-87039767
46	TAF7	chr3:87039856-87040619	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:87039553-87040598	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr3:87040280-87040678	IMR90	lung:	n/a	n/a
49	TBP	chr3:87039618-87040783	H1-hESC	embryonic stem cell:	n/a	n/a
50	CEBPB	chr3:87039259-87040932	Hela-S3	cervix:	n/a	chr3:87039403-87039415

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:87039890..87040592-chr6:34759297..34760271,2	Hela-S3	cervix:

Variant related genes	Relation type
VGLL3	TF binding region
ENSG00000065060	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1025631	0.80[EUR][1000 genomes]
rs1436638	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1836918	0.84[EUR][1000 genomes]
rs2043663	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2575774	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2575775	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2660777	0.80[EUR][1000 genomes]
rs2660799	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1000548	chr3:87034157-87331360	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv3340343	chr3:87038787-87041635	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87033000-87041000	Active TSS	Placenta	Placenta
2	chr3:87033800-87041200	Active TSS	HSMMtube	muscle
3	chr3:87034800-87040600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:87035400-87041000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:87035600-87040600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:87035800-87041200	Active TSS	Ovary	ovary
7	chr3:87035800-87041400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:87036200-87041000	Active TSS	Right Atrium	heart
9	chr3:87036800-87040600	Active TSS	NHLF	lung
10	chr3:87037000-87041000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:87037000-87041200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:87037200-87040600	Active TSS	Placenta Amnion	Placenta Amnion
13	chr3:87037200-87040800	Active TSS	HSMM	muscle
14	chr3:87037200-87041000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:87037400-87040600	Active TSS	Osteobl	bone
16	chr3:87037400-87040800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr3:87037600-87040800	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:87037600-87040800	Active TSS	Hela-S3	cervix
19	chr3:87037600-87041200	Active TSS	Fetal Lung	lung
20	chr3:87038000-87041000	Active TSS	Aorta	Aorta
21	chr3:87038200-87041000	Active TSS	Colon Smooth Muscle	Colon
22	chr3:87038400-87041000	Active TSS	Right Ventricle	heart
23	chr3:87038600-87040600	Active TSS	NH-A	brain
24	chr3:87038600-87040800	Active TSS	A549	lung
25	chr3:87038600-87040800	Active TSS	NHDF-Ad	bronchial
26	chr3:87038600-87041000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:87038800-87040600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
28	chr3:87039000-87040600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:87039000-87041000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:87039000-87041000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr3:87039200-87040400	Bivalent/Poised TSS	Fetal Brain Female	brain
32	chr3:87039200-87040400	Bivalent/Poised TSS	Small Intestine	intestine
33	chr3:87039200-87040600	Bivalent Enhancer	Fetal Heart	heart
34	chr3:87039200-87041000	Active TSS	Brain Substantia Nigra	brain
35	chr3:87039400-87040600	Bivalent/Poised TSS	Colonic Mucosa	Colon
36	chr3:87039400-87040800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:87039400-87040800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
38	chr3:87039400-87040800	Active TSS	Gastric	stomach
39	chr3:87039400-87041000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:87039400-87041000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr3:87039400-87041200	Active TSS	Fetal Intestine Large	intestine
42	chr3:87039600-87040400	Bivalent Enhancer	Liver	Liver
43	chr3:87039600-87040600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:87039600-87040600	Bivalent Enhancer	Fetal Brain Male	brain
45	chr3:87039600-87040600	Bivalent/Poised TSS	HepG2	liver
46	chr3:87039600-87040800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:87039600-87040800	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr3:87039600-87041000	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:87039600-87041000	Active TSS	Brain Anterior Caudate	brain
50	chr3:87039600-87041000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain

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