Variant report

Variant	rs2962991
Chromosome Location	chr15:57348776-57348777
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	chr15:57344217..57346725-chr15:57347528..57349236,2	K562	blood:

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1037956	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10467927	0.86[YRI][hapmap]
rs10518894	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10518895	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11071309	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11630195	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11631541	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11632069	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11635645	0.83[EUR][1000 genomes]
rs11637955	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11852340	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11853331	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11855648	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11856411	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs11857507	0.95[JPT][hapmap]
rs11858471	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11858783	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12898327	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12898844	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12899036	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12899187	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12899915	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12900589	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12900874	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12900986	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12904634	0.95[JPT][hapmap]
rs12904933	0.95[JPT][hapmap]
rs12905900	0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12906042	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs12906873	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12909811	0.81[ASN][1000 genomes]
rs12910094	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12912210	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12912868	0.95[JPT][hapmap]
rs12914425	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs12916237	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs12916958	0.81[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs12917247	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs13313455	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs13379847	0.93[YRI][hapmap]
rs1430820	0.93[YRI][hapmap]
rs1430822	0.93[YRI][hapmap]
rs1430823	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1628067	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs16977222	0.86[AFR][1000 genomes]
rs17239040	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs17819700	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1814585	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1820995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867641	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs213149	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2169466	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2264904	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290938	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2414490	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2414491	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2414492	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2435907	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439919	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2464429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2464431	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2585082	0.90[JPT][hapmap]
rs2585087	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2585088	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]
rs2585102	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2585112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2615231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2703576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703577	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2703580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2733170	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733171	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2733174	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733176	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2733182	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733185	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733307	0.83[EUR][1000 genomes]
rs2733332	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs28414972	0.84[EUR][1000 genomes]
rs28422021	0.83[AFR][1000 genomes]
rs28514688	0.84[EUR][1000 genomes]
rs28533433	0.83[AFR][1000 genomes]
rs28541606	0.83[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920269	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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];0.98[ASN][1000 genomes]
rs2951898	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2951899	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]
rs2951901	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]
rs2951903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951906	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2957574	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2957591	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2962990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2962992	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	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34262415	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3794613	0.95[JPT][hapmap]
rs3803454	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs3803455	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4559854	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4774250	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs4774898	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4774902	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4774910	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4774913	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs62022988	0.83[ASN][1000 genomes]
rs6493901	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6493902	0.96[YRI][hapmap]
rs715338	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7161965	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7162194	0.89[YRI][hapmap]
rs7163267	0.93[YRI][hapmap]
rs7164655	0.86[YRI][hapmap]
rs7168387	0.84[EUR][1000 genomes]
rs7169053	0.80[AFR][1000 genomes]
rs7171073	0.85[AFR][1000 genomes]
rs7171304	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs7173936	0.80[EUR][1000 genomes]
rs7175436	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs7176873	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs7178833	0.85[YRI][hapmap]
rs745652	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7496293	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs8034066	0.96[YRI][hapmap]
rs8037901	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs8039899	0.96[YRI][hapmap]
rs967514	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs978274	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs9806170	0.93[YRI][hapmap]
rs9806199	0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2962991	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
3	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
5	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
6	chr15:57328600-57355000	Weak transcription	Dnd41	blood
7	chr15:57329800-57349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:57329800-57351400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:57332000-57349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:57332000-57349400	Weak transcription	Thymus	Thymus
11	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:57333400-57349400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:57335400-57349000	Weak transcription	NHEK	skin
14	chr15:57336600-57349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:57336600-57371800	Weak transcription	K562	blood
16	chr15:57336800-57349000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:57337400-57349200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:57337600-57351200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:57338200-57350000	Weak transcription	Fetal Heart	heart
20	chr15:57339200-57350000	Weak transcription	HSMM	muscle
21	chr15:57339600-57349800	Weak transcription	Primary T cells from cord blood	blood
22	chr15:57339600-57349800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:57339600-57355600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:57339800-57361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:57341600-57348800	Weak transcription	Osteobl	bone
27	chr15:57341800-57349000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57341800-57349400	Weak transcription	NH-A	brain
29	chr15:57341800-57349800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:57342000-57349000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
32	chr15:57344000-57348800	Weak transcription	Ovary	ovary
33	chr15:57344000-57349200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:57344000-57349200	Weak transcription	GM12878-XiMat	blood
35	chr15:57344000-57349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:57344000-57351400	Weak transcription	Fetal Brain Female	brain
37	chr15:57344400-57351400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
39	chr15:57345200-57349200	Weak transcription	NHDF-Ad	bronchial
40	chr15:57345600-57349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:57346000-57349000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:57346000-57349200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:57346200-57348800	Weak transcription	Adipose Nuclei	Adipose
45	chr15:57346200-57348800	Weak transcription	Left Ventricle	heart
46	chr15:57346200-57349000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:57346200-57349400	Weak transcription	Small Intestine	intestine
48	chr15:57346400-57352800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:57346600-57349200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:57346600-57349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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