Variant report

Variant	rs2951901
Chromosome Location	chr15:57336750-57336751
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	chr15:57331807..57334195-chr15:57336717..57338701,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

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];0.91[JPT][hapmap]
rs11631541	0.80[CHB][hapmap];0.95[JPT][hapmap]
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]
rs11857507	0.95[JPT][hapmap]
rs11858471	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11858783	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12898327	0.82[CEU][hapmap];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	0.82[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];0.91[JPT][hapmap]
rs12904933	0.95[JPT][hapmap]
rs12905900	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12906042	0.94[JPT][hapmap]
rs12906873	0.80[CHB][hapmap];0.91[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	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs12916958	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs12917247	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13313455	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs1430823	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1628067	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[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];0.85[YRI][hapmap];0.81[AFR][1000 genomes];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	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2169466	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2264904	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290938	0.80[CHB][hapmap];0.91[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	0.85[AFR][1000 genomes];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];0.98[ASN][1000 genomes]
rs2439919	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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];0.97[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	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2470079	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585082	0.91[JPT][hapmap]
rs2585087	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2585088	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]
rs2585102	0.96[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];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733170	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733171	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733174	0.96[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];0.95[ASN][1000 genomes]
rs2733177	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733182	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733185	0.95[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];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2733307	0.82[EUR][1000 genomes]
rs2733332	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs28414972	0.83[EUR][1000 genomes]
rs28514688	0.83[EUR][1000 genomes]
rs28648502	0.83[EUR][1000 genomes]
rs2920264	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920265	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2927189	0.87[EUR][1000 genomes]
rs2951895	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2951898	0.87[EUR][1000 genomes]
rs2951899	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2951903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2951904	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2951906	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957574	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957591	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2962990	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[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];0.97[ASN][1000 genomes]
rs2962992	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2962993	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34262415	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3803454	0.91[JPT][hapmap]
rs3803455	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs4559854	0.86[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];0.83[ASN][1000 genomes]
rs6493901	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs715338	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs7161965	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7168387	0.84[EUR][1000 genomes]
rs7175436	0.96[CEU][hapmap];0.90[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
rs2951901	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
2	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57324200-57337800	Weak transcription	Psoas Muscle	Psoas
4	chr15:57324200-57339000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:57324200-57341200	Weak transcription	Fetal Stomach	stomach
6	chr15:57324400-57338000	Weak transcription	HSMM	muscle
7	chr15:57324400-57341200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
10	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:57324800-57347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
13	chr15:57326400-57341000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
15	chr15:57328400-57341200	Weak transcription	Ovary	ovary
16	chr15:57328400-57343800	Weak transcription	Small Intestine	intestine
17	chr15:57328400-57345800	Weak transcription	Left Ventricle	heart
18	chr15:57328600-57355000	Weak transcription	Dnd41	blood
19	chr15:57329800-57349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:57329800-57351400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:57330400-57343400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:57330600-57337000	Weak transcription	Fetal Thymus	thymus
23	chr15:57330800-57337400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr15:57331800-57338200	Enhancers	Brain Cingulate Gyrus	brain
25	chr15:57331800-57341200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:57332000-57337000	Weak transcription	GM12878-XiMat	blood
27	chr15:57332000-57337800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:57332000-57345200	Weak transcription	HepG2	liver
29	chr15:57332000-57346000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr15:57332000-57349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:57332000-57349400	Weak transcription	Thymus	Thymus
32	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr15:57332800-57343800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:57332800-57345800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:57333000-57337200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:57333000-57337200	Weak transcription	Fetal Lung	lung
37	chr15:57333200-57337200	Weak transcription	Brain Germinal Matrix	brain
38	chr15:57333200-57341200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:57333400-57349400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:57334000-57337600	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:57334000-57341000	Weak transcription	NH-A	brain
42	chr15:57334000-57345000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:57334000-57346000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:57334000-57346200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:57334200-57337200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:57334200-57343600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:57335000-57347400	Weak transcription	Lung	lung
48	chr15:57335200-57338000	Weak transcription	Esophagus	oesophagus
49	chr15:57335200-57338200	Enhancers	Fetal Heart	heart
50	chr15:57335200-57341400	Weak transcription	Fetal Kidney	kidney

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