Variant report

Variant	rs2962992
Chromosome Location	chr15:57346505-57346506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57344217..57346725-chr15:57347528..57349236,2	K562	blood:

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1037956	0.95[JPT][hapmap]
rs1037958	0.90[JPT][hapmap];0.81[TSI][hapmap]
rs10467927	0.82[YRI][hapmap]
rs10518894	0.80[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs10518895	0.90[JPT][hapmap]
rs10518899	0.89[TSI][hapmap]
rs11071309	0.90[JPT][hapmap]
rs11630195	0.85[JPT][hapmap];0.91[TSI][hapmap]
rs11631541	0.90[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs11632069	0.90[JPT][hapmap]
rs11635645	0.83[EUR][1000 genomes]
rs11637955	0.90[JPT][hapmap]
rs11852340	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11853331	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs11855648	0.90[JPT][hapmap]
rs11856411	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs11857507	0.89[JPT][hapmap]
rs11858471	0.85[JPT][hapmap]
rs11858783	0.95[JPT][hapmap]
rs12050751	0.88[TSI][hapmap]
rs12898327	0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12898844	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12899036	0.90[JPT][hapmap]
rs12899187	0.85[JPT][hapmap]
rs12899915	0.85[JPT][hapmap]
rs12900589	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs12900874	0.80[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12900986	0.85[JPT][hapmap];0.91[TSI][hapmap]
rs12904602	0.89[TSI][hapmap]
rs12904634	0.90[JPT][hapmap]
rs12904933	0.90[JPT][hapmap]
rs12905900	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12906042	0.87[JPT][hapmap]
rs12906873	0.85[JPT][hapmap];0.91[TSI][hapmap]
rs12909811	0.82[ASN][1000 genomes]
rs12910094	0.90[JPT][hapmap]
rs12912210	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs12912868	0.90[JPT][hapmap]
rs12914425	0.89[JPT][hapmap]
rs12916237	0.82[JPT][hapmap]
rs12916958	0.90[JPT][hapmap]
rs12917247	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13313455	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs13379847	0.89[YRI][hapmap]
rs1430820	0.89[YRI][hapmap]
rs1430822	0.89[YRI][hapmap]
rs1430823	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1628067	0.84[CEU][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs16977222	0.88[AFR][1000 genomes]
rs17239040	0.85[JPT][hapmap]
rs17819700	0.85[JPT][hapmap]
rs1814585	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs1820995	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867641	0.90[JPT][hapmap];0.81[TSI][hapmap]
rs213149	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs2169466	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2264904	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290938	0.95[JPT][hapmap];0.81[TSI][hapmap]
rs2414490	0.85[JPT][hapmap]
rs2414491	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs2414492	0.90[JPT][hapmap]
rs2435907	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439919	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2464429	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2464430	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2464431	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470079	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470082	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585082	0.85[JPT][hapmap];0.91[TSI][hapmap]
rs2585087	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2585088	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]
rs2585102	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2585112	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2615231	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs2703576	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703577	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703580	0.84[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733170	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733171	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2733174	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733176	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733182	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733185	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733188	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2733307	0.83[EUR][1000 genomes]
rs2733332	0.89[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs28414972	0.84[EUR][1000 genomes]
rs28422021	0.85[AFR][1000 genomes]
rs28514688	0.84[EUR][1000 genomes]
rs28533433	0.85[AFR][1000 genomes]
rs28541606	0.85[AFR][1000 genomes]
rs28648502	0.84[EUR][1000 genomes]
rs2920264	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920265	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920267	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920269	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2927189	0.88[EUR][1000 genomes]
rs2951895	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2951898	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2951899	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]
rs2951901	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]
rs2951903	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2951904	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2951906	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957574	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957591	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2962990	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2962991	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2962993	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34262415	0.85[JPT][hapmap];0.88[TSI][hapmap]
rs3794613	0.90[JPT][hapmap]
rs3803454	0.85[JPT][hapmap]
rs3803455	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs4559854	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4774250	0.85[JPT][hapmap]
rs4774898	0.85[JPT][hapmap]
rs4774902	0.85[JPT][hapmap]
rs4774910	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs4774913	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs62022988	0.82[ASN][1000 genomes]
rs6493901	0.89[JPT][hapmap]
rs6493902	0.84[LWK][hapmap];0.86[YRI][hapmap]
rs715338	0.80[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs7161965	0.90[JPT][hapmap]
rs7162194	0.85[YRI][hapmap]
rs7163267	0.89[YRI][hapmap]
rs7164655	0.82[YRI][hapmap]
rs7168387	0.84[EUR][1000 genomes]
rs7169053	0.82[AFR][1000 genomes]
rs7171073	0.86[AFR][1000 genomes]
rs7171304	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs7173936	0.80[EUR][1000 genomes]
rs7175436	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap]
rs7176873	0.83[ASW][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs7178833	0.85[LWK][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs745652	0.90[JPT][hapmap];0.89[TSI][hapmap]
rs7496293	0.85[JPT][hapmap]
rs8034066	0.96[YRI][hapmap]
rs8037901	0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs8039899	0.92[YRI][hapmap]
rs967514	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs978274	0.90[JPT][hapmap];0.81[TSI][hapmap]
rs9806170	0.96[MKK][hapmap];0.89[YRI][hapmap]
rs9806199	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2962992	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs2962992	GCOM1	cis	cerebellum	SCAN

Chromatin state (count:92 , 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	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
4	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:57324800-57347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
7	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
8	chr15:57328600-57355000	Weak transcription	Dnd41	blood
9	chr15:57329800-57349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:57329800-57351400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:57332000-57349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:57332000-57349400	Weak transcription	Thymus	Thymus
13	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:57333400-57349400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:57335000-57347400	Weak transcription	Lung	lung
16	chr15:57335400-57349000	Weak transcription	NHEK	skin
17	chr15:57336600-57349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:57336600-57371800	Weak transcription	K562	blood
19	chr15:57336800-57349000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:57337400-57349200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:57337600-57351200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:57338200-57350000	Weak transcription	Fetal Heart	heart
23	chr15:57339200-57350000	Weak transcription	HSMM	muscle
24	chr15:57339600-57349800	Weak transcription	Primary T cells from cord blood	blood
25	chr15:57339600-57349800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:57339600-57355600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:57339800-57361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:57341000-57347000	Enhancers	Brain Substantia Nigra	brain
30	chr15:57341600-57348800	Weak transcription	Osteobl	bone
31	chr15:57341800-57349000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:57341800-57349400	Weak transcription	NH-A	brain
33	chr15:57341800-57349800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:57342000-57349000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
36	chr15:57344000-57348800	Weak transcription	Ovary	ovary
37	chr15:57344000-57349200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:57344000-57349200	Weak transcription	GM12878-XiMat	blood
39	chr15:57344000-57349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:57344000-57351400	Weak transcription	Fetal Brain Female	brain
41	chr15:57344400-57351400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:57344600-57348200	Enhancers	Brain Hippocampus Middle	brain
43	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
44	chr15:57345000-57346600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:57345000-57346800	Enhancers	Colon Smooth Muscle	Colon
46	chr15:57345000-57347000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr15:57345000-57348000	Enhancers	Brain Angular Gyrus	brain
48	chr15:57345200-57346800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr15:57345200-57346800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr15:57345200-57346800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links