Variant report

Variant	rs2039509
Chromosome Location	chr6:131180122-131180123
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	FOXA1	chr6:131179744-131180465	HepG2	liver:	n/a	n/a
2	MYBL2	chr6:131179185-131180313	HepG2	liver:	n/a	n/a
3	EP300	chr6:131179877-131180429	HepG2	liver:	n/a	n/a
4	SP1	chr6:131179925-131180370	HepG2	liver:	n/a	n/a
5	FOXA1	chr6:131180008-131180444	HepG2	liver:	n/a	n/a
6	USF1	chr6:131180029-131180293	HepG2	liver:	n/a	chr6:131180183-131180194
7	HNF4A	chr6:131179858-131180207	HepG2	liver:	n/a	n/a
8	KAP1	chr6:131178831-131180442	HEK293	kidney:	n/a	n/a
9	USF1	chr6:131180019-131180281	HepG2	liver:	n/a	chr6:131180183-131180194
10	EP300	chr6:131179827-131180346	HepG2	liver:	n/a	n/a
11	FOXA2	chr6:131179902-131180344	HepG2	liver:	n/a	n/a
12	TEAD4	chr6:131179682-131180453	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1006655	0.84[CEU][hapmap]
rs10499180	1.00[CHB][hapmap]
rs1114644	0.84[CEU][hapmap];0.90[ASN][1000 genomes]
rs11968011	1.00[CHB][hapmap]
rs11968295	1.00[ASN][1000 genomes]
rs12333037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13217139	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1334689	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1406456	1.00[CHB][hapmap]
rs1413753	0.84[EUR][1000 genomes]
rs1571911	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1582055	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs17060018	1.00[CHB][hapmap]
rs1977577	1.00[CHB][hapmap]
rs1999474	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2008598	0.86[EUR][1000 genomes]
rs2027117	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2039830	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2105250	0.82[CEU][hapmap]
rs2183969	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs2184408	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs2236080	0.90[ASN][1000 genomes]
rs2839942	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs3777439	1.00[ASN][1000 genomes]
rs3777446	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4075265	0.93[EUR][1000 genomes]
rs4895897	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs4895898	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4897475	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs55825065	1.00[ASN][1000 genomes]
rs56287869	1.00[ASN][1000 genomes]
rs58072193	1.00[ASN][1000 genomes]
rs60609111	0.90[ASN][1000 genomes]
rs6536	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs6569706	0.92[EUR][1000 genomes]
rs6569709	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6569711	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6906068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6907284	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs6907608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6908154	0.85[EUR][1000 genomes]
rs6908659	0.85[EUR][1000 genomes]
rs6910788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6914649	0.90[ASN][1000 genomes]
rs6921455	0.86[EUR][1000 genomes]
rs6922872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6933789	0.90[ASN][1000 genomes]
rs6938309	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6938735	0.93[EUR][1000 genomes]
rs6940163	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs73629702	1.00[ASN][1000 genomes]
rs73631003	1.00[ASN][1000 genomes]
rs73632204	1.00[ASN][1000 genomes]
rs73632239	1.00[ASN][1000 genomes]
rs73774316	1.00[ASN][1000 genomes]
rs73774318	1.00[ASN][1000 genomes]
rs73774322	1.00[ASN][1000 genomes]
rs73775303	0.90[ASN][1000 genomes]
rs73775313	1.00[ASN][1000 genomes]
rs73775315	1.00[ASN][1000 genomes]
rs73775327	1.00[ASN][1000 genomes]
rs73775329	0.90[ASN][1000 genomes]
rs73775330	1.00[ASN][1000 genomes]
rs73775331	1.00[ASN][1000 genomes]
rs73775333	1.00[ASN][1000 genomes]
rs761835	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs7738572	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7741462	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7747303	1.00[ASN][1000 genomes]
rs7748468	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7754229	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7754351	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs7761655	0.84[CEU][hapmap]
rs7762876	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7763473	0.86[EUR][1000 genomes]
rs7764383	0.90[ASN][1000 genomes]
rs7766004	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7766505	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7766938	1.00[CHB][hapmap]
rs7768048	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7769310	0.84[EUR][1000 genomes]
rs7773093	0.90[EUR][1000 genomes]
rs7774832	0.84[EUR][1000 genomes]
rs7775288	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs871628	1.00[CHB][hapmap]
rs9285468	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9321256	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9375777	0.94[EUR][1000 genomes]
rs9375786	0.84[CEU][hapmap]
rs9388858	0.85[EUR][1000 genomes]
rs9388867	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9388870	0.90[CEU][hapmap]
rs9388871	0.90[CEU][hapmap]
rs9402298	0.86[EUR][1000 genomes]
rs9402304	0.84[CEU][hapmap]
rs9402305	0.84[CEU][hapmap]
rs9483190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9492764	0.89[CEU][hapmap]
rs955191	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs988749	0.81[EUR][1000 genomes]
rs998228	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131149400-131213200	Weak transcription	Pancreas	Pancrea
2	chr6:131150600-131183400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:131151600-131216600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:131158200-131190600	Weak transcription	Spleen	Spleen
5	chr6:131158200-131214400	Weak transcription	Lung	lung
6	chr6:131159000-131229000	Weak transcription	Colonic Mucosa	Colon
7	chr6:131161000-131186600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:131161800-131186400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:131168400-131190600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:131168800-131214600	Weak transcription	Fetal Kidney	kidney
11	chr6:131170000-131189000	Strong transcription	Adipose Nuclei	Adipose
12	chr6:131170400-131181200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:131170400-131193000	Weak transcription	Fetal Thymus	thymus
14	chr6:131170400-131217400	Weak transcription	Psoas Muscle	Psoas
15	chr6:131170600-131184600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:131170600-131187000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:131170600-131190400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:131170600-131192600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:131170600-131193000	Weak transcription	Primary T cells from cord blood	blood
20	chr6:131170600-131213800	Weak transcription	GM12878-XiMat	blood
21	chr6:131170800-131189000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr6:131171200-131209600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:131171200-131223200	Weak transcription	Right Ventricle	heart
24	chr6:131171400-131220200	Weak transcription	Fetal Brain Male	brain
25	chr6:131172600-131185600	Weak transcription	Gastric	stomach
26	chr6:131172600-131186600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:131172800-131183400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:131172800-131189400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:131173000-131207000	Weak transcription	Brain Substantia Nigra	brain
30	chr6:131173200-131185200	Weak transcription	Thymus	Thymus
31	chr6:131173400-131190800	Weak transcription	Esophagus	oesophagus
32	chr6:131174400-131185600	Weak transcription	Primary B cells from cord blood	blood
33	chr6:131175000-131182000	Weak transcription	Placenta	Placenta
34	chr6:131175000-131185400	Weak transcription	Aorta	Aorta
35	chr6:131175000-131222400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:131175200-131180400	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:131175200-131181200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:131175200-131181800	Weak transcription	Ovary	ovary
39	chr6:131175200-131190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:131175200-131190600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:131175200-131214000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:131175400-131183600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:131175400-131185400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:131175400-131188000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:131175400-131194200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:131175400-131203600	Weak transcription	A549	lung
47	chr6:131175400-131211200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:131175600-131183400	Weak transcription	Osteobl	bone
49	chr6:131175600-131185600	Weak transcription	HSMMtube	muscle
50	chr6:131175600-131188200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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