Variant report

Variant	rs2585088
Chromosome Location	chr15:57328867-57328868
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57285454..57287142-chr15:57328507..57331190,2	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1037956	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10518894	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10518895	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11071309	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11630195	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11631541	0.80[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11632069	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11635645	0.82[EUR][1000 genomes]
rs11637955	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11852340	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11853331	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs11855648	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs11858471	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11858783	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12898327	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12898844	0.85[ASN][1000 genomes]
rs12899036	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12899187	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12899915	0.91[JPT][hapmap]
rs12900589	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12900874	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900986	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12905900	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906042	0.94[JPT][hapmap]
rs12906873	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12910094	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12912210	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs12914425	0.95[JPT][hapmap]
rs12916237	0.90[JPT][hapmap]
rs12916958	0.81[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs12917247	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13313455	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs1430823	0.81[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1628067	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17239040	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs17819700	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1814585	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs1820995	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867641	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs213149	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2169466	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2264904	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290938	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2414490	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2414491	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2414492	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2435907	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439918	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439919	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2464429	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2464430	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464431	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470082	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585082	0.90[JPT][hapmap]
rs2585087	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2585102	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2585112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2615231	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2703576	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703577	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703580	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733171	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733174	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733176	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733177	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2733182	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733185	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733307	0.82[EUR][1000 genomes]
rs2733332	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28414972	0.83[EUR][1000 genomes]
rs28514688	0.83[EUR][1000 genomes]
rs28648502	0.83[EUR][1000 genomes]
rs2920264	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2920265	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2920269	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2927189	0.87[EUR][1000 genomes]
rs2951895	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951898	0.87[EUR][1000 genomes]
rs2951899	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2951901	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2951903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951904	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951906	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957574	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957591	0.87[EUR][1000 genomes]
rs2962990	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2962991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2962992	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2962993	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34262415	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3803454	0.91[JPT][hapmap]
rs3803455	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs4559854	0.84[AMR][1000 genomes]
rs4774250	0.82[JPT][hapmap]
rs4774898	0.91[JPT][hapmap]
rs4774902	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4774910	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4774913	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs62022988	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493901	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs715338	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7161965	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7168387	0.84[EUR][1000 genomes]
rs7175436	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs745652	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs7496293	0.91[JPT][hapmap]
rs8037901	0.81[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap]
rs967514	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs978274	0.80[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2585088	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57309400-57334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
3	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:57318600-57331000	Weak transcription	Fetal Kidney	kidney
5	chr15:57318600-57335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:57323800-57329400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:57324200-57329400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr15:57324200-57331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:57324200-57331800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:57324200-57332600	Weak transcription	Fetal Lung	lung
11	chr15:57324200-57337800	Weak transcription	Psoas Muscle	Psoas
12	chr15:57324200-57339000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:57324200-57341200	Weak transcription	Fetal Stomach	stomach
14	chr15:57324400-57332600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:57324400-57338000	Weak transcription	HSMM	muscle
16	chr15:57324400-57341200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:57324600-57331400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
20	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:57324800-57347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
23	chr15:57325000-57334600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:57325400-57332600	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:57326400-57341000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:57326600-57331200	Weak transcription	HepG2	liver
27	chr15:57326600-57331400	Weak transcription	Brain Angular Gyrus	brain
28	chr15:57326800-57332400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:57327200-57329200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr15:57327200-57332600	Weak transcription	Liver	Liver
31	chr15:57327600-57329200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr15:57327600-57329400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:57327600-57330200	Enhancers	Brain Substantia Nigra	brain
34	chr15:57327600-57330400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr15:57327800-57329000	Enhancers	Brain Cingulate Gyrus	brain
36	chr15:57327800-57329200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr15:57327800-57330200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr15:57327800-57330200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:57327800-57332600	Enhancers	Brain Hippocampus Middle	brain
40	chr15:57328000-57329200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:57328000-57330200	Enhancers	Primary T cells from cord blood	blood
42	chr15:57328000-57330200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr15:57328200-57329800	Enhancers	HSMMtube	muscle
44	chr15:57328200-57330200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr15:57328200-57330400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:57328200-57330400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
48	chr15:57328400-57329000	Weak transcription	Brain Germinal Matrix	brain
49	chr15:57328400-57329200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr15:57328400-57329400	Enhancers	Fetal Heart	heart

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