Variant report

Variant	rs12898327
Chromosome Location	chr15:57363937-57363938
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1037956	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518894	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10518895	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518899	0.92[CEU][hapmap]
rs11071305	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11071309	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11630195	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11631228	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11631541	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11632069	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11637955	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11852340	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11853331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11855648	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11857507	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11858471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11858783	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12050751	0.96[CEU][hapmap]
rs12898844	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899036	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12899187	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12899915	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900589	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12900874	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900986	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12901780	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12903578	0.86[AMR][1000 genomes]
rs12904070	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12904602	0.89[CEU][hapmap]
rs12904634	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12904933	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12905900	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12906042	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12906873	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12906936	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908670	0.86[AMR][1000 genomes]
rs12909811	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12912007	0.85[EUR][1000 genomes]
rs12912210	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12912868	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12914182	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914410	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12914425	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12914625	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12915473	0.85[AMR][1000 genomes]
rs12915489	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12916237	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12916958	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12917247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13313455	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1430823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462156	0.93[CEU][hapmap]
rs1545728	0.95[JPT][hapmap]
rs1628067	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17239040	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17239508	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17819700	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1814585	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1820995	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1867641	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2053472	0.86[AMR][1000 genomes]
rs2111891	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2116065	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2116066	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs213149	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs213164	0.86[AMR][1000 genomes]
rs2169466	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2290938	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2414490	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414491	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2414492	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2414494	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2435907	0.80[ASN][1000 genomes]
rs2439918	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2464429	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2464430	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs2470079	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2470082	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2583108	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2585082	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2585087	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2585088	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2585102	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2585112	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2615231	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2703576	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703577	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703580	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733170	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2733171	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733174	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733176	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2733177	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733181	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2733182	0.81[ASN][1000 genomes]
rs2733185	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733188	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2733332	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2920267	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920269	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2951895	0.82[ASN][1000 genomes]
rs2951899	0.85[JPT][hapmap]
rs2951901	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2951903	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2951904	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2962990	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2962991	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2962992	0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2962993	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34262415	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35646942	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3794613	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3803454	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3803455	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4238321	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4353440	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4774250	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4774898	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4774899	0.88[AMR][1000 genomes]
rs4774902	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs4774910	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4774913	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62022986	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62022988	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62025331	0.89[AMR][1000 genomes]
rs6493901	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs715338	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7161965	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7170133	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7175436	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs745652	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7496293	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8037901	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs967514	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs978274	0.85[CEU][hapmap];1.00[CHB][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
rs12898327	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 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	chr15:57336600-57371800	Weak transcription	K562	blood
3	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
9	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
10	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:57350400-57374000	Weak transcription	Ovary	ovary
12	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:57353400-57371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:57353600-57364200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:57353800-57364800	Weak transcription	HSMM	muscle
16	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
17	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:57354600-57371600	Weak transcription	NH-A	brain
20	chr15:57355000-57374000	Weak transcription	Osteobl	bone
21	chr15:57355400-57365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
23	chr15:57356400-57364400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:57356400-57370800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:57356400-57371000	Weak transcription	Dnd41	blood
26	chr15:57356400-57371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:57356600-57364800	Weak transcription	Fetal Kidney	kidney
29	chr15:57356600-57372000	Weak transcription	Primary B cells from cord blood	blood
30	chr15:57356800-57371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:57357600-57366600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:57357600-57371600	Weak transcription	HUVEC	blood vessel
33	chr15:57360200-57371800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:57360400-57364000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:57360400-57364800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:57360400-57372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:57360600-57371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:57360800-57364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:57361400-57365800	Enhancers	Brain Anterior Caudate	brain
40	chr15:57361600-57365000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr15:57361600-57365600	Enhancers	Brain Hippocampus Middle	brain
42	chr15:57361800-57365400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:57362000-57365000	Weak transcription	Primary T cells from cord blood	blood
44	chr15:57362000-57366200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:57362200-57364400	Weak transcription	Fetal Heart	heart
46	chr15:57362200-57364600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:57362200-57364600	Weak transcription	HMEC	breast
48	chr15:57362200-57364600	Weak transcription	NHEK	skin
49	chr15:57362200-57365000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:57362400-57365000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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