Variant report

Variant	rs7512545
Chromosome Location	chr1:57001400-57001401
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	chr1:57001074-57001432	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr1:57000570-57001415	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr1:57000742-57001595	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr1:57000909-57001537	H1-hESC	embryonic stem cell:	n/a	chr1:57001245-57001252
5	MAX	chr1:57000684-57001530	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr1:57000989-57001521	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:56999856-57001768	PFSK-1	brain:	n/a	n/a
8	TEAD4	chr1:57000997-57001642	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAFK	chr1:57001084-57001509	H1-hESC	embryonic stem cell:	n/a	chr1:57001290-57001304 chr1:57001292-57001303 chr1:57001291-57001302 chr1:57001292-57001303 chr1:57001291-57001307 chr1:57001291-57001302
10	TAF1	chr1:57001084-57001506	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:56999993-57001990	H1-hESC	embryonic stem cell:	n/a	n/a
12	GTF2F1	chr1:57000967-57001430	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr1:57001009-57001454	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr1:57001075-57001599	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF1	chr1:57000914-57001415	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr1:57000729-57001894	H1-hESC	embryonic stem cell:	n/a	n/a
17	ATF2	chr1:57000839-57001494	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr1:57000631-57001512	H1-hESC	embryonic stem cell:	n/a	n/a
19	ATF2	chr1:57000803-57001526	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:57001022-57001541	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr1:57001088-57001492	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr1:57000822-57001442	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr1:57000892-57001444	H1-hESC	embryonic stem cell:	n/a	n/a
24	ZNF143	chr1:57000982-57001613	H1-hESC	embryonic stem cell:	n/a	chr1:57001375-57001394
25	EP300	chr1:57000956-57001430	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:57001098-57001639	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:56998973-57004163	HepG2	liver:	n/a	n/a
28	SIN3A	chr1:57000889-57001468	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF2	chr1:57000974-57001703	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RPL21P23	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10157636	1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs10888977	0.81[JPT][hapmap]
rs10888979	0.90[LWK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs11206839	0.95[LWK][hapmap];0.98[MKK][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes]
rs11206840	0.92[AFR][1000 genomes]
rs11206841	0.93[LWK][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes]
rs11583161	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590570	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12081589	0.84[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[ASN][1000 genomes]
rs12084507	0.94[ASN][1000 genomes]
rs1759752	0.81[JPT][hapmap]
rs4912314	0.95[JPT][hapmap]
rs57966457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58289463	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60314060	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6690245	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72664330	0.94[ASN][1000 genomes]
rs7515808	0.95[JPT][hapmap]
rs7519268	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549894	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7554557	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
3	chr1:56990000-57004000	Genic enhancers	Liver	Liver
4	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
5	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
6	chr1:56993200-57001400	Enhancers	Right Atrium	heart
7	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
8	chr1:56993800-57004200	Weak transcription	NH-A	brain
9	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
10	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
11	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
12	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:56995000-57003600	Strong transcription	Osteobl	bone
16	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:56995800-57004000	Genic enhancers	HepG2	liver
19	chr1:56996000-57002800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:56996200-57003000	Genic enhancers	H1 Cell Line	embryonic stem cell
21	chr1:56996200-57003000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:56996200-57003000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:56996600-57004000	Strong transcription	HSMM	muscle
24	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:56996800-57003000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:56997000-57001800	Genic enhancers	Adipose Nuclei	Adipose
27	chr1:56997000-57003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:56997200-57002600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
30	chr1:56997400-57002600	Strong transcription	Lung	lung
31	chr1:56997400-57002800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr1:56997600-57002000	Genic enhancers	Fetal Thymus	thymus
33	chr1:56997600-57004400	Genic enhancers	Fetal Muscle Leg	muscle
34	chr1:56997800-57002600	Genic enhancers	Brain Anterior Caudate	brain
35	chr1:56997800-57003600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:56998000-57002800	Genic enhancers	Left Ventricle	heart
37	chr1:56998600-57002200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:56998600-57003800	Strong transcription	Fetal Stomach	stomach
39	chr1:56998800-57001400	Weak transcription	Small Intestine	intestine
40	chr1:56998800-57002000	Genic enhancers	Thymus	Thymus
41	chr1:56998800-57002600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:56999000-57001600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:56999000-57002400	Strong transcription	Aorta	Aorta
44	chr1:56999200-57001400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:56999200-57002600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:56999400-57001800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:56999400-57001800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:56999400-57002600	Genic enhancers	Brain Substantia Nigra	brain
49	chr1:56999400-57002800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:56999400-57012800	Weak transcription	HSMMtube	muscle

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