Variant report

Variant	rs17082910
Chromosome Location	chr4:54357641-54357642
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	CTCF	chr4:54357602-54357729	GM12878	blood:	n/a	n/a
2	SMC3	chr4:54356522-54357757	SK-N-SH	brain:	n/a	n/a
3	ZNF384	chr4:54357206-54357719	K562	blood:	n/a	n/a
4	CTCF	chr4:54356955-54357723	SK-N-SH	brain:	n/a	chr4:54357364-54357382
5	CTCF	chr4:54357630-54357708	Gliobla	brain:	n/a	n/a
6	CTCF	chr4:54357640-54357790	GM12872	blood:	n/a	n/a
7	CTCF	chr4:54357109-54357700	HCT-116	colon:	n/a	chr4:54357364-54357382
8	ZNF384	chr4:54357184-54357677	GM12878	blood:	n/a	n/a
9	CTCF	chr4:54357560-54357710	GM12870	blood:	n/a	n/a
10	CTCF	chr4:54357620-54357770	GM12873	blood:	n/a	n/a
11	MAFK	chr4:54357082-54357760	IMR90	lung:	n/a	chr4:54357578-54357593
12	NFYB	chr4:54357363-54357731	GM12878	blood:	n/a	chr4:54357551-54357565 chr4:54357552-54357565
13	CTCF	chr4:54357520-54357670	WI-38	lung:	n/a	n/a
14	USF2	chr4:54357468-54357665	GM12878	blood:	n/a	n/a
15	CTCF	chr4:54357520-54357670	HepG2	liver:	n/a	n/a
16	RAD21	chr4:54357208-54357645	GM12878	blood:	n/a	n/a
17	MAFF	chr4:54357004-54357738	K562	blood:	n/a	chr4:54357128-54357142
18	MAFK	chr4:54357148-54357677	K562	blood:	n/a	chr4:54357578-54357593
19	MAFK	chr4:54357175-54357749	HepG2	liver:	n/a	chr4:54357578-54357593
20	MAFF	chr4:54357119-54357751	HepG2	liver:	n/a	chr4:54357128-54357142
21	MAFK	chr4:54357240-54357781	H1-hESC	embryonic stem cell:	n/a	chr4:54357578-54357593
22	CTCF	chr4:54357600-54357750	AG04449	skin:	n/a	n/a
23	RAD21	chr4:54357144-54357648	MCF-7	breast:	n/a	n/a
24	MAFK	chr4:54357123-54357746	HepG2	liver:	n/a	chr4:54357578-54357593
25	RAD21	chr4:54357174-54357684	IMR90	lung:	n/a	n/a
26	RAD21	chr4:54356625-54357986	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr4:54356720-54357716	A549	lung:	n/a	chr4:54357364-54357382

No.	Distal block	Cell Line	Cell type
1	chr4:54357078..54357883-chr4:54467415..54468360,4	MCF-7	breast:
2	chr4:54357356..54357868-chr4:55094218..55094869,2	K562	blood:
3	chr4:54353594..54355161-chr4:54356979..54358658,2	MCF-7	breast:
4	chr4:54355457..54358448-chr4:54362389..54364275,2	K562	blood:

Variant related genes	Relation type
LNX1-AS1	TF binding region
ENSG00000250930	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10008334	0.82[EUR][1000 genomes]
rs10012853	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10013573	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028214	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1014056	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10517291	0.86[CHB][hapmap]
rs10517292	0.86[CHB][hapmap]
rs10517296	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11133267	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11935822	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11942086	0.80[EUR][1000 genomes]
rs11944047	0.82[EUR][1000 genomes]
rs11946199	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12499401	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12501431	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12507723	0.82[EUR][1000 genomes]
rs13117240	0.82[EUR][1000 genomes]
rs13119372	0.82[EUR][1000 genomes]
rs13120051	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13125807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13130836	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1351514	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1399241	0.82[EUR][1000 genomes]
rs17082565	0.85[CHB][hapmap]
rs17082659	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2128103	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2271555	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2271557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34028346	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34173240	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34317954	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35033239	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35089532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35225781	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35313782	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36090882	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3946758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3986364	0.81[EUR][1000 genomes]
rs4864747	0.85[CHB][hapmap]
rs6420001	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6554095	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs6554096	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs6554103	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6554108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6834099	0.82[EUR][1000 genomes]
rs6835629	0.82[EUR][1000 genomes]
rs6846569	0.82[EUR][1000 genomes]
rs6847289	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71597836	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7678953	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679743	0.85[ASN][1000 genomes]
rs7684450	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7684894	0.82[EUR][1000 genomes]
rs7694840	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs980988	0.81[ASN][1000 genomes]
rs997832	0.84[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9992820	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9997358	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9997844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
5	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
6	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
7	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
10	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
11	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
14	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:54348000-54362200	Weak transcription	Fetal Intestine Large	intestine
16	chr4:54348200-54359600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:54349000-54360000	Weak transcription	Liver	Liver
18	chr4:54352800-54361800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:54352800-54362000	Weak transcription	Esophagus	oesophagus
20	chr4:54353600-54362000	Weak transcription	Gastric	stomach
21	chr4:54353600-54362000	Weak transcription	Pancreas	Pancrea
22	chr4:54354600-54358000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:54355000-54357800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:54355000-54357800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:54355000-54357800	Enhancers	Osteobl	bone
26	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
27	chr4:54356400-54357800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:54356400-54357800	Enhancers	HSMMtube	muscle
29	chr4:54356600-54357800	Enhancers	Fetal Lung	lung
30	chr4:54356600-54357800	Enhancers	Fetal Stomach	stomach
31	chr4:54356600-54373400	Weak transcription	Right Atrium	heart
32	chr4:54356800-54357800	Enhancers	Adipose Nuclei	Adipose
33	chr4:54356800-54357800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:54356800-54362400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:54357000-54357800	Enhancers	Stomach Mucosa	stomach
36	chr4:54357200-54357800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:54357200-54357800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:54357200-54357800	Enhancers	NHDF-Ad	bronchial
39	chr4:54357200-54357800	Enhancers	NHLF	lung
40	chr4:54357200-54362600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:54357400-54357800	Enhancers	Ovary	ovary
42	chr4:54357400-54363000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:54357600-54357800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:54357600-54357800	Enhancers	Fetal Muscle Leg	muscle
45	chr4:54357600-54358800	Enhancers	Placenta	Placenta
46	chr4:54357600-54362200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:54357600-54362800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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