Variant report

Variant	rs12040095
Chromosome Location	chr1:220393414-220393415
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	chr1:220393124-220394371	GM19193	blood:	n/a	n/a
2	MAX	chr1:220393248-220394399	GM12878	blood:	n/a	n/a
3	RELA	chr1:220392905-220394171	GM18505	blood:	n/a	n/a
4	POLR2A	chr1:220393157-220394042	GM12891	blood:	n/a	n/a
5	RELA	chr1:220393090-220394264	GM18951	blood:	n/a	n/a
6	BHLHE40	chr1:220393088-220394303	GM12878	blood:	n/a	n/a
7	TCF12	chr1:220393376-220393659	GM12878	blood:	n/a	n/a
8	BCL11A	chr1:220393179-220393498	GM12878	blood:	n/a	n/a
9	PML	chr1:220393317-220393839	GM12878	blood:	n/a	n/a
10	YY1	chr1:220393140-220394427	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:220393042-220394396	GM12878	blood:	n/a	n/a
12	BCLAF1	chr1:220393159-220393955	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:220392696-220394773	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:220392888-220394883	GM12878	blood:	n/a	n/a
15	RCOR1	chr1:220393123-220394003	GM12878	blood:	n/a	n/a
16	MAFK	chr1:220393066-220393467	H1-hESC	embryonic stem cell:	n/a	chr1:220393268-220393283 chr1:220393272-220393283
17	MAFK	chr1:220393113-220393445	K562	blood:	n/a	chr1:220393268-220393283 chr1:220393272-220393283
18	WRNIP1	chr1:220392914-220394406	GM12878	blood:	n/a	n/a
19	ZNF143	chr1:220392882-220394040	GM12878	blood:	n/a	n/a
20	RELA	chr1:220392954-220394221	GM10847	blood:	n/a	n/a
21	RELA	chr1:220392977-220394164	GM12878	blood:	n/a	n/a
22	RUNX3	chr1:220393083-220394147	GM12878	blood:	n/a	n/a
23	TAF1	chr1:220393378-220393674	GM12891	blood:	n/a	n/a
24	TAF1	chr1:220393398-220393736	GM12878	blood:	n/a	n/a
25	POU2F2	chr1:220393048-220393818	GM12891	blood:	n/a	chr1:220393431-220393444
26	EP300	chr1:220393082-220393773	GM12878	blood:	n/a	chr1:220393288-220393295
27	ZNF384	chr1:220393310-220393545	GM12878	blood:	n/a	n/a
28	FOXM1	chr1:220393060-220394232	GM12878	blood:	n/a	n/a
29	RUNX3	chr1:220393030-220394557	GM12878	blood:	n/a	n/a
30	POU2F2	chr1:220393096-220393803	GM12891	blood:	n/a	chr1:220393431-220393444
31	POLR2A	chr1:220393007-220394503	GM12892	blood:	n/a	n/a
32	MAFK	chr1:220392026-220394150	GM12878	blood:	n/a	chr1:220393268-220393283 chr1:220393272-220393283
33	MXI1	chr1:220392940-220394856	GM12878	blood:	n/a	n/a
34	RELA	chr1:220393147-220394330	GM15510	blood:	n/a	n/a
35	STAT1	chr1:220393146-220393902	GM12878	blood:	n/a	n/a
36	TAF1	chr1:220393373-220393787	GM12878	blood:	n/a	n/a
37	MAFK	chr1:220393099-220393448	HepG2	liver:	n/a	chr1:220393268-220393283 chr1:220393272-220393283
38	STAT5A	chr1:220393008-220393978	GM12878	blood:	n/a	n/a
39	RELA	chr1:220393203-220393738	GM18526	blood:	n/a	n/a
40	MEF2C	chr1:220393188-220393783	GM12878	blood:	n/a	chr1:220393384-220393398 chr1:220393437-220393452 chr1:220393379-220393400
41	POLR2A	chr1:220393400-220393946	GM12878	blood:	n/a	n/a
42	RELA	chr1:220393172-220394213	GM12892	blood:	n/a	n/a
43	NFATC1	chr1:220393052-220394164	GM12878	blood:	n/a	n/a
44	RELA	chr1:220392861-220394201	GM19099	blood:	n/a	n/a
45	USF2	chr1:220393068-220393824	GM12878	blood:	n/a	n/a
46	MAFF	chr1:220393114-220393451	HepG2	liver:	n/a	chr1:220393267-220393285
47	POLR2A	chr1:220393396-220393752	GM12891	blood:	n/a	n/a
48	MEF2A	chr1:220393166-220393790	GM12878	blood:	n/a	chr1:220393384-220393398 chr1:220393379-220393400
49	POLR2A	chr1:220392822-220394486	GM12892	blood:	n/a	n/a
50	STAT3	chr1:220392519-220394056	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000270708	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10127631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779401	0.83[EUR][1000 genomes]
rs10863539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863540	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118506	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118510	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118513	0.83[EUR][1000 genomes]
rs11586671	0.83[EUR][1000 genomes]
rs12022336	0.91[ASN][1000 genomes]
rs12025326	0.91[ASN][1000 genomes]
rs12025702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12026270	0.91[ASN][1000 genomes]
rs12030504	1.00[ASN][1000 genomes]
rs12031256	0.82[ASN][1000 genomes]
rs12032536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032738	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12033612	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12037712	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12039349	0.91[ASN][1000 genomes]
rs12043920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12045447	0.82[ASN][1000 genomes]
rs12086105	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007139	0.87[GIH][hapmap]
rs28650887	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820455	0.87[GIH][hapmap]
rs56357312	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6690426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6703091	0.83[EUR][1000 genomes]
rs73087829	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73095623	0.83[EUR][1000 genomes]
rs73095636	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73098540	0.82[ASN][1000 genomes]
rs73098550	0.82[ASN][1000 genomes]
rs73098551	0.82[ASN][1000 genomes]
rs73098553	0.82[ASN][1000 genomes]
rs73098567	0.82[ASN][1000 genomes]
rs73098569	0.91[ASN][1000 genomes]
rs73098579	0.91[ASN][1000 genomes]
rs874331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220325000-220398400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:220374600-220407600	Weak transcription	Fetal Brain Male	brain
3	chr1:220378800-220398200	Weak transcription	Psoas Muscle	Psoas
4	chr1:220378800-220398200	Weak transcription	Small Intestine	intestine
5	chr1:220379000-220418200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:220379200-220397600	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:220379200-220400400	Weak transcription	Right Ventricle	heart
8	chr1:220379200-220409600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:220379200-220410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:220379200-220422600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:220380400-220393600	Weak transcription	Lung	lung
12	chr1:220380400-220398200	Weak transcription	Brain Anterior Caudate	brain
13	chr1:220380400-220400800	Weak transcription	Spleen	Spleen
14	chr1:220381200-220422000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:220384000-220399400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:220384200-220396400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:220384200-220398200	Weak transcription	Aorta	Aorta
18	chr1:220384200-220398200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:220384200-220398600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:220384200-220398800	Weak transcription	Fetal Intestine Small	intestine
21	chr1:220384200-220400000	Weak transcription	Pancreas	Pancrea
22	chr1:220384200-220400200	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:220384200-220400400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:220384200-220402800	Weak transcription	NHLF	lung
25	chr1:220384200-220404400	Weak transcription	Ovary	ovary
26	chr1:220384200-220408800	Weak transcription	A549	lung
27	chr1:220384200-220420600	Weak transcription	Fetal Kidney	kidney
28	chr1:220384200-220423000	Weak transcription	Esophagus	oesophagus
29	chr1:220384200-220425800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:220384400-220398200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:220384400-220400200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:220384400-220413400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:220384600-220394600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:220384800-220393600	Weak transcription	Gastric	stomach
35	chr1:220384800-220398000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:220384800-220398200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:220384800-220398800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:220384800-220398800	Weak transcription	Fetal Intestine Large	intestine
39	chr1:220384800-220399000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:220384800-220399000	Weak transcription	Colonic Mucosa	Colon
41	chr1:220384800-220400000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:220384800-220400000	Weak transcription	Left Ventricle	heart
43	chr1:220384800-220400800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:220384800-220401000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:220384800-220401800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:220384800-220404400	Weak transcription	HSMMtube	muscle
47	chr1:220384800-220408000	Weak transcription	Hela-S3	cervix
48	chr1:220384800-220417000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:220385000-220396000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:220385000-220403400	Weak transcription	Rectal Mucosa Donor 29	rectum

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