Variant report

Variant	rs1462156
Chromosome Location	chr15:57503423-57503424
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	chr15:57501438..57503633-chr15:57503718..57505515,2	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1037956	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1037958	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10518894	0.85[CEU][hapmap]
rs10518895	0.86[CEU][hapmap]
rs10518899	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071309	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11629653	0.81[EUR][1000 genomes]
rs11630910	0.81[EUR][1000 genomes]
rs11631084	0.84[EUR][1000 genomes]
rs11631541	0.85[CEU][hapmap]
rs11632069	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs11633061	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11634352	0.81[EUR][1000 genomes]
rs11635440	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs11636201	0.97[EUR][1000 genomes]
rs11636340	0.84[EUR][1000 genomes]
rs11636348	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11636919	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11637955	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11852340	0.85[CEU][hapmap]
rs11853331	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11855648	0.89[CEU][hapmap]
rs11856055	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856073	0.85[EUR][1000 genomes]
rs11857507	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11857722	0.85[EUR][1000 genomes]
rs11858783	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11858880	0.90[EUR][1000 genomes]
rs12050751	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050758	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898327	0.93[CEU][hapmap]
rs12898356	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899036	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12899588	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12900589	0.85[CEU][hapmap]
rs12900874	0.91[CEU][hapmap]
rs12901671	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12902099	0.85[EUR][1000 genomes]
rs12902170	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12902581	0.83[EUR][1000 genomes]
rs12903115	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12903151	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12903221	0.84[EUR][1000 genomes]
rs12903578	0.82[EUR][1000 genomes]
rs12904189	0.85[EUR][1000 genomes]
rs12904321	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12904501	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12904561	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12904602	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904634	0.92[CEU][hapmap]
rs12904933	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs12905900	0.81[CEU][hapmap]
rs12906042	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12906335	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906566	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12908278	0.81[EUR][1000 genomes]
rs12908760	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12909016	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12910094	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12910556	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910832	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12911256	0.85[EUR][1000 genomes]
rs12911297	0.81[EUR][1000 genomes]
rs12911518	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912210	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912353	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12912392	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912868	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12914182	0.80[EUR][1000 genomes]
rs12914410	0.82[EUR][1000 genomes]
rs12914425	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12914481	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12915473	0.81[EUR][1000 genomes]
rs12915489	0.85[EUR][1000 genomes]
rs12916478	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917093	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12917247	0.93[CEU][hapmap]
rs1430823	0.93[CEU][hapmap]
rs1545728	0.85[EUR][1000 genomes]
rs17239431	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17239508	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1814585	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1867641	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs2278685	0.85[EUR][1000 genomes]
rs2290938	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2414491	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2414492	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414494	0.84[EUR][1000 genomes]
rs2414497	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2593235	0.81[EUR][1000 genomes]
rs2593237	0.97[EUR][1000 genomes]
rs2593238	0.98[EUR][1000 genomes]
rs2703596	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733332	0.82[CEU][hapmap]
rs2733341	0.81[EUR][1000 genomes]
rs3095821	0.88[CEU][hapmap]
rs3794613	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4238321	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs4238322	0.81[EUR][1000 genomes]
rs4303429	0.85[EUR][1000 genomes]
rs4353440	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4369592	0.85[EUR][1000 genomes]
rs4447362	0.85[EUR][1000 genomes]
rs4774250	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774251	0.81[EUR][1000 genomes]
rs4774252	0.81[EUR][1000 genomes]
rs4774910	0.93[CEU][hapmap]
rs4774913	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774918	0.81[EUR][1000 genomes]
rs4774919	0.81[EUR][1000 genomes]
rs5014892	0.84[EUR][1000 genomes]
rs61996955	0.82[EUR][1000 genomes]
rs62022237	0.91[EUR][1000 genomes]
rs6493901	0.92[CEU][hapmap]
rs7161965	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs745652	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8033118	0.96[ASN][1000 genomes]
rs8037901	0.92[CEU][hapmap]
rs898901	0.88[EUR][1000 genomes]
rs935326	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs960946	0.82[EUR][1000 genomes]
rs978274	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1462156	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57444400-57507400	Weak transcription	K562	blood
2	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
4	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
5	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
7	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
10	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
11	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:57490600-57505800	Weak transcription	NH-A	brain
16	chr15:57491000-57505600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:57491000-57506000	Weak transcription	HMEC	breast
18	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:57491400-57505800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:57491400-57505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:57491400-57506000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr15:57491400-57506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:57491400-57510000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:57491400-57510000	Weak transcription	Psoas Muscle	Psoas
25	chr15:57491400-57510200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:57491400-57511200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:57491600-57505200	Weak transcription	NHLF	lung
28	chr15:57491600-57506000	Weak transcription	Fetal Stomach	stomach
29	chr15:57491600-57508000	Weak transcription	HUVEC	blood vessel
30	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
31	chr15:57492000-57504200	Weak transcription	Brain Substantia Nigra	brain
32	chr15:57492000-57505200	Weak transcription	Fetal Kidney	kidney
33	chr15:57492400-57504200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:57492400-57504800	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:57492400-57511600	Weak transcription	Left Ventricle	heart
36	chr15:57493600-57504800	Weak transcription	Brain Germinal Matrix	brain
37	chr15:57493600-57506000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:57494000-57504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:57494000-57505400	Weak transcription	HSMM	muscle
40	chr15:57494000-57506000	Weak transcription	Fetal Intestine Large	intestine
41	chr15:57494000-57506000	Weak transcription	A549	lung
42	chr15:57494200-57505800	Weak transcription	HepG2	liver
43	chr15:57494200-57508600	Weak transcription	Dnd41	blood
44	chr15:57494400-57504400	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:57494800-57506200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:57495000-57506000	Weak transcription	Stomach Mucosa	stomach
47	chr15:57495600-57506200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:57496400-57505000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:57496400-57506000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:57496400-57508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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