Variant report

Variant	rs2951899
Chromosome Location	chr15:57381851-57381852
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	chr15:57370971..57373246-chr15:57380194..57383118,2	K562	blood:
2	chr15:57364693..57367235-chr15:57380279..57382303,2	K562	blood:

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1037956	0.90[JPT][hapmap]
rs1037958	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs10467927	0.88[YRI][hapmap]
rs10518894	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10518895	0.86[JPT][hapmap]
rs10518899	0.89[TSI][hapmap]
rs11071305	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11071309	0.86[JPT][hapmap]
rs11630195	0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11631541	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs11632069	0.86[JPT][hapmap]
rs11635440	0.86[JPT][hapmap]
rs11635645	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636100	0.81[ASN][1000 genomes]
rs11637955	0.85[JPT][hapmap]
rs11852340	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11853331	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs11855648	0.86[JPT][hapmap]
rs11856411	0.92[YRI][hapmap]
rs11857507	0.89[JPT][hapmap]
rs11858471	0.81[JPT][hapmap]
rs11858783	0.85[JPT][hapmap]
rs12050751	0.89[TSI][hapmap]
rs12898327	0.85[JPT][hapmap]
rs12899036	0.86[JPT][hapmap]
rs12899187	0.81[JPT][hapmap]
rs12899915	0.81[JPT][hapmap]
rs12900589	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900874	0.81[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs12900986	0.81[JPT][hapmap];0.91[TSI][hapmap]
rs12904602	0.89[TSI][hapmap]
rs12904634	0.86[JPT][hapmap];0.80[TSI][hapmap]
rs12904933	0.86[JPT][hapmap]
rs12905900	0.81[JPT][hapmap]
rs12906042	0.87[JPT][hapmap]
rs12906873	0.81[JPT][hapmap];0.91[TSI][hapmap]
rs12909402	0.82[ASN][1000 genomes]
rs12910094	0.85[JPT][hapmap]
rs12910170	0.83[ASN][1000 genomes]
rs12912210	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs12912868	0.86[JPT][hapmap]
rs12914425	0.89[JPT][hapmap]
rs12916958	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs12917247	0.86[JPT][hapmap]
rs13313455	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13379847	0.96[YRI][hapmap]
rs1430820	0.88[YRI][hapmap]
rs1430822	0.88[YRI][hapmap]
rs1430823	0.81[JPT][hapmap]
rs1545728	0.90[JPT][hapmap]
rs1628067	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap]
rs17239040	0.81[JPT][hapmap]
rs17239508	0.85[JPT][hapmap]
rs17819700	0.81[JPT][hapmap]
rs1814585	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs1820995	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs1867641	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs213149	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2169465	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2169466	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2264904	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290938	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs2414490	0.81[JPT][hapmap]
rs2414491	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2414492	0.86[JPT][hapmap]
rs2435907	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2439918	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2439919	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2464429	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2464430	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2470079	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2470082	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2585082	0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2585087	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2585088	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2585102	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs2585112	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2615231	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2703576	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2703577	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2703580	0.84[ASW][hapmap];0.92[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733170	0.92[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs2733171	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2733174	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs2733177	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733182	0.87[EUR][1000 genomes]
rs2733185	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2733188	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733307	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733332	0.89[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28414972	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28514688	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28648502	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28712697	0.88[AFR][1000 genomes]
rs2920264	0.84[EUR][1000 genomes]
rs2920265	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2920267	0.92[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2920269	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2927189	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951895	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2951898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2951901	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2951903	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2951904	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2951906	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957574	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957591	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2962990	0.84[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2962991	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2962992	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2962993	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs3095821	0.86[JPT][hapmap];0.84[TSI][hapmap]
rs34262415	0.81[JPT][hapmap];0.89[TSI][hapmap]
rs3794613	0.86[JPT][hapmap]
rs3803454	0.81[JPT][hapmap]
rs3803455	0.81[JPT][hapmap];0.86[TSI][hapmap]
rs4238321	0.80[JPT][hapmap]
rs4774898	0.81[JPT][hapmap]
rs4774902	0.81[JPT][hapmap]
rs4774910	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4774913	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs6493901	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6493902	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs67077316	0.81[AFR][1000 genomes]
rs715338	0.81[JPT][hapmap];0.89[TSI][hapmap]
rs7161965	0.86[JPT][hapmap]
rs7162194	0.91[YRI][hapmap]
rs7163267	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs7164655	0.88[YRI][hapmap]
rs7168387	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171304	0.90[YRI][hapmap]
rs7173936	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7175436	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs7176873	0.83[ASW][hapmap];0.83[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap]
rs7178833	0.89[MKK][hapmap];0.88[YRI][hapmap]
rs745652	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs7496293	0.81[JPT][hapmap]
rs8034066	1.00[YRI][hapmap]
rs8037901	0.81[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8039899	0.92[YRI][hapmap]
rs935326	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs967514	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs978274	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs9806170	0.96[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9806199	0.96[YRI][hapmap];0.81[AFR][1000 genomes]

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
rs2951899	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
5	chr15:57362800-57384200	Weak transcription	HepG2	liver
6	chr15:57363800-57382000	Weak transcription	Right Atrium	heart
7	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:57365600-57385200	Weak transcription	HSMM	muscle
9	chr15:57365800-57384000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:57371800-57382400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:57372000-57384000	Weak transcription	Dnd41	blood
12	chr15:57372600-57386000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
14	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:57372800-57384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:57372800-57384000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:57372800-57384400	Weak transcription	Liver	Liver
18	chr15:57372800-57386000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:57373000-57382000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:57373000-57384600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:57373000-57385400	Weak transcription	Primary B cells from cord blood	blood
23	chr15:57373200-57384200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:57373200-57384600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:57374000-57385000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr15:57374400-57382000	Weak transcription	Psoas Muscle	Psoas
27	chr15:57374400-57389400	Weak transcription	NHEK	skin
28	chr15:57374600-57382200	Weak transcription	Left Ventricle	heart
29	chr15:57374600-57382600	Weak transcription	Adipose Nuclei	Adipose
30	chr15:57374600-57384000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:57374600-57386000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:57374600-57390000	Weak transcription	HMEC	breast
33	chr15:57374600-57398600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:57374800-57384400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:57374800-57386800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:57374800-57387800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:57374800-57397800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:57374800-57409600	Weak transcription	Osteobl	bone
39	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
40	chr15:57375000-57385000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:57375000-57386200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:57375000-57386200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:57375000-57393400	Weak transcription	Fetal Intestine Small	intestine
44	chr15:57375000-57398000	Weak transcription	NH-A	brain
45	chr15:57375000-57398400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:57376200-57385800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr15:57376200-57406000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr15:57376600-57386200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:57376800-57382400	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:57376800-57384000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links