Variant report

Variant	rs10518894
Chromosome Location	chr15:57403598-57403599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57403095..57404934-chr15:57406973..57408733,2	K562	blood:
2	chr15:57397844..57400555-chr15:57402758..57405029,3	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1037956	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	0.86[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10518895	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518899	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs11071305	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11071309	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11630195	0.86[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs11631541	0.86[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.80[TSI][hapmap]
rs11632069	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11635440	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11635645	0.96[ASN][1000 genomes]
rs11636100	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637955	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11852340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853331	0.86[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855648	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857507	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11858471	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11858783	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12050751	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs12898327	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12899036	0.86[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12899187	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12899904	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12899915	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs12900038	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900589	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12900874	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12900986	0.86[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs12903578	0.85[AFR][1000 genomes]
rs12904602	0.85[TSI][hapmap]
rs12904634	0.86[ASW][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12904933	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12905900	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12906042	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12906873	0.86[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs12909402	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910094	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910170	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912007	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912210	0.86[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap]
rs12912868	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12914182	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12914410	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914425	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12915489	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs12916237	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs12916958	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12917247	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13313455	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1430823	0.80[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1462156	0.85[CEU][hapmap]
rs1545728	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1628067	0.91[JPT][hapmap]
rs17239040	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs17239508	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17819700	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1814585	0.86[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1820995	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1867641	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs213149	0.90[JPT][hapmap]
rs2169465	0.93[ASN][1000 genomes]
rs2169466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290938	0.86[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs2414490	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2414491	0.86[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs2414492	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2414494	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2464429	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2464430	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2470079	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2470082	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2585082	0.85[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs2585087	0.95[JPT][hapmap]
rs2585088	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2585102	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2585112	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2615231	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2703576	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2703580	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2733170	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2733171	0.95[JPT][hapmap]
rs2733174	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2733188	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2733307	0.96[ASN][1000 genomes]
rs2733332	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs28414972	0.86[ASN][1000 genomes]
rs28514688	0.86[ASN][1000 genomes]
rs28648502	0.87[ASN][1000 genomes]
rs2920267	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2927189	0.87[ASN][1000 genomes]
rs2951898	0.81[ASN][1000 genomes]
rs2951899	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2951901	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2951903	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2951904	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2957591	0.86[ASN][1000 genomes]
rs2962990	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2962991	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2962992	0.80[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2962993	0.91[JPT][hapmap]
rs3095821	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs34262415	0.86[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs3794613	0.86[ASW][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3803454	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3803455	0.80[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4238321	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4353440	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4774250	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4774902	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4774910	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774913	0.86[ASW][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6493901	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs715338	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7161965	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7168387	0.86[ASN][1000 genomes]
rs7175436	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs745652	0.86[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs7496293	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs8037901	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs935326	0.86[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs967514	0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs978274	0.86[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10518894	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
3	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:57374800-57409600	Weak transcription	Osteobl	bone
6	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
7	chr15:57376200-57406000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:57381200-57404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:57381200-57409400	Weak transcription	NHLF	lung
11	chr15:57382600-57403800	Weak transcription	Left Ventricle	heart
12	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:57382800-57404400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:57382800-57404400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:57382800-57419600	Weak transcription	K562	blood
16	chr15:57383000-57404000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:57384200-57409200	Weak transcription	Brain Germinal Matrix	brain
18	chr15:57384600-57404400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:57384600-57405600	Weak transcription	Brain Anterior Caudate	brain
20	chr15:57384600-57410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:57385200-57406200	Weak transcription	HepG2	liver
22	chr15:57386200-57410200	Weak transcription	Ovary	ovary
23	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr15:57386600-57404000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:57386800-57405600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:57387000-57404400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:57387000-57406400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
30	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:57387400-57403800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:57387400-57406000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr15:57387400-57406200	Weak transcription	HUVEC	blood vessel
34	chr15:57387600-57409400	Weak transcription	Dnd41	blood
35	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
36	chr15:57388000-57404200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:57388200-57406200	Weak transcription	A549	lung
38	chr15:57389000-57404400	Weak transcription	HSMM	muscle
39	chr15:57390200-57409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:57391200-57404400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:57391200-57410200	Weak transcription	HMEC	breast
42	chr15:57391400-57409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:57391800-57404400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:57392600-57406000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:57392800-57406000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:57393800-57404400	Weak transcription	Thymus	Thymus
47	chr15:57394400-57406000	Weak transcription	Lung	lung
48	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
49	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
50	chr15:57399000-57404400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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