Variant report

Variant	rs869934
Chromosome Location	chr1:56999393-56999394
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	MEF2A	chr1:56999264-56999573	GM12878	blood:	n/a	chr1:56999425-56999446 chr1:56999425-56999446
2	CHD2	chr1:56998974-56999581	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:56998833-56999719	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:56999367-56999505	H1-hESC	embryonic stem cell:	n/a	n/a
5	BCL11A	chr1:56999315-56999692	GM12878	blood:	n/a	n/a
6	BATF	chr1:56999315-56999627	GM12878	blood:	n/a	n/a
7	FOS	chr1:56999336-56999786	MCF10A-Er-Src	breast:	n/a	chr1:56999646-56999654
8	GATA3	chr1:56999256-56999433	SH-SY5Y	brain:	n/a	n/a
9	BATF	chr1:56999230-56999684	GM12878	blood:	n/a	n/a
10	STAT5A	chr1:56999242-56999652	GM12878	blood:	n/a	n/a
11	NFYB	chr1:56999369-56999635	GM12878	blood:	n/a	n/a
12	BHLHE40	chr1:56998818-56999581	GM12878	blood:	n/a	n/a
13	FOXM1	chr1:56999187-56999721	GM12878	blood:	n/a	n/a
14	MEF2A	chr1:56999347-56999711	GM12878	blood:	n/a	chr1:56999425-56999446 chr1:56999425-56999446
15	MTA3	chr1:56999205-56999758	GM12878	blood:	n/a	n/a
16	IRF4	chr1:56999175-56999653	GM12878	blood:	n/a	n/a
17	ATF2	chr1:56999317-56999659	GM12878	blood:	n/a	n/a
18	WRNIP1	chr1:56999322-56999506	GM12878	blood:	n/a	n/a
19	FOS	chr1:56999371-56999678	MCF10A-Er-Src	breast:	n/a	chr1:56999646-56999654
20	ATF2	chr1:56999228-56999729	GM12878	blood:	n/a	n/a
21	FOS	chr1:56999376-56999783	MCF10A-Er-Src	breast:	n/a	chr1:56999646-56999654
22	MTA3	chr1:56999303-56999710	GM12878	blood:	n/a	n/a
23	EBF1	chr1:56999341-56999579	GM12878	blood:	n/a	n/a
24	BCL3	chr1:56999306-56999702	GM12878	blood:	n/a	n/a
25	NFATC1	chr1:56999245-56999659	GM12878	blood:	n/a	n/a
26	RUNX3	chr1:56999196-56999675	GM12878	blood:	n/a	n/a
27	POU2F2	chr1:56999373-56999644	GM12891	blood:	n/a	n/a
28	STAT3	chr1:56999376-56999585	MCF10A-Er-Src	breast:	n/a	n/a
29	PML	chr1:56999146-56999839	GM12878	blood:	n/a	n/a
30	ZNF143	chr1:56999305-56999501	GM12878	blood:	n/a	n/a
31	EP300	chr1:56999200-56999671	GM12878	blood:	n/a	n/a
32	NFIC	chr1:56999150-56999832	GM12878	blood:	n/a	n/a
33	TCF12	chr1:56999327-56999592	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:56998973-57004163	HepG2	liver:	n/a	n/a
35	FOS	chr1:56999334-56999784	MCF10A-Er-Src	breast:	n/a	chr1:56999646-56999654
36	IKZF1	chr1:56999289-56999950	GM12878	blood:	n/a	n/a
37	MEF2C	chr1:56999213-56999649	GM12878	blood:	n/a	chr1:56999425-56999446 chr1:56999425-56999446
38	NFIC	chr1:56999308-56999664	GM12878	blood:	n/a	n/a
39	EP300	chr1:56998999-56999703	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56996284..56998415-chr1:56998780..57000786,2	MCF-7	breast:
2	chr1:56998583..57000958-chr1:57003015..57004640,2	K562	blood:

Variant related genes	Relation type
RPL21P23	TF binding region
ENSG00000236776	Chromatin interaction

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

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

rs_ID	r²[population]
rs10443239	0.88[ASN][1000 genomes]
rs10493211	1.00[JPT][hapmap]
rs10789026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11206831	1.00[JPT][hapmap]
rs11206832	1.00[JPT][hapmap]
rs11206834	0.88[ASN][1000 genomes]
rs11206835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206838	1.00[JPT][hapmap]
rs11576602	1.00[JPT][hapmap]
rs11582172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12134109	1.00[JPT][hapmap]
rs12402226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406517	1.00[JPT][hapmap]
rs1572057	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2404717	0.88[ASN][1000 genomes]
rs3738570	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3927762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7528118	1.00[JPT][hapmap]
rs7551402	1.00[JPT][hapmap]
rs8016	1.00[JPT][hapmap]

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:100 , 50 per page) page: 1 2

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	chr1:56983400-57000800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
4	chr1:56990000-57004000	Genic enhancers	Liver	Liver
5	chr1:56992000-57001200	Weak transcription	Spleen	Spleen
6	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
7	chr1:56993000-56999800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
9	chr1:56993200-57001400	Enhancers	Right Atrium	heart
10	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
11	chr1:56993800-57004200	Weak transcription	NH-A	brain
12	chr1:56994000-57000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:56994000-57001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
15	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
16	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
17	chr1:56994200-56999400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:56994200-57001200	Weak transcription	Dnd41	blood
19	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:56994600-56999600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:56994600-56999800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:56995000-57003600	Strong transcription	Osteobl	bone
25	chr1:56995200-56999800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:56995200-57000000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:56995600-57000000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:56995800-57004000	Genic enhancers	HepG2	liver
31	chr1:56996000-57001200	Enhancers	Right Ventricle	heart
32	chr1:56996000-57002800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:56996200-57003000	Genic enhancers	H1 Cell Line	embryonic stem cell
34	chr1:56996200-57003000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:56996200-57003000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:56996400-56999400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:56996400-57000200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:56996600-56999400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:56996600-57000000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:56996600-57004000	Strong transcription	HSMM	muscle
41	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:56996800-57000800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:56996800-57003000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:56997000-57001800	Genic enhancers	Adipose Nuclei	Adipose
45	chr1:56997000-57003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:56997200-57002600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
48	chr1:56997400-56999400	Genic enhancers	Fetal Intestine Large	intestine
49	chr1:56997400-57002600	Strong transcription	Lung	lung
50	chr1:56997400-57002800	Strong transcription	Placenta Amnion	Placenta Amnion

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