Variant report

Variant	rs10518899
Chromosome Location	chr15:57491182-57491183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57489288..57492189-chr15:57492368..57494008,2	MCF-7	breast:
2	chr15:57489296..57493196-chr15:57493593..57496438,4	K562	blood:
3	chr15:57484373..57486425-chr15:57489732..57491739,3	K562	blood:

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

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

rs_ID	r²[population]
rs1037956	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1037958	0.92[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10518894	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs10518895	0.85[CEU][hapmap]
rs11071309	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11629653	0.80[EUR][1000 genomes]
rs11630195	0.96[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs11630910	0.80[EUR][1000 genomes]
rs11631084	0.83[EUR][1000 genomes]
rs11631541	0.89[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11632069	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11633061	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11634352	0.80[EUR][1000 genomes]
rs11635440	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11636201	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11636340	0.83[EUR][1000 genomes]
rs11636348	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11636919	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11637955	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852340	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs11853331	0.96[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs11855648	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs11856055	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856073	0.84[EUR][1000 genomes]
rs11857507	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11857722	0.84[EUR][1000 genomes]
rs11858783	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858880	0.91[EUR][1000 genomes]
rs12050751	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050758	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898327	0.92[CEU][hapmap]
rs12898356	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899036	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899588	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12899915	0.96[CEU][hapmap]
rs12900589	0.85[CEU][hapmap]
rs12900874	0.87[CEU][hapmap]
rs12901671	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902099	0.84[EUR][1000 genomes]
rs12902170	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902581	0.82[EUR][1000 genomes]
rs12903115	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12903151	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12903221	0.83[EUR][1000 genomes]
rs12903578	0.83[EUR][1000 genomes]
rs12904189	0.84[EUR][1000 genomes]
rs12904321	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12904501	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12904561	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12904602	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904634	0.88[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs12904933	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12905900	0.96[CEU][hapmap]
rs12906042	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12906335	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12906566	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12906873	0.96[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs12908278	0.80[EUR][1000 genomes]
rs12908760	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12909016	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12910094	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12910556	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12910832	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12911256	0.84[EUR][1000 genomes]
rs12911518	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912210	0.88[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12912353	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12912392	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912868	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12914182	0.81[EUR][1000 genomes]
rs12914410	0.83[EUR][1000 genomes]
rs12914425	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12914481	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12915473	0.82[EUR][1000 genomes]
rs12915489	0.84[EUR][1000 genomes]
rs12916478	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12917093	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12917247	0.92[CEU][hapmap]
rs1430823	0.92[CEU][hapmap]
rs1462156	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]
rs1545728	0.84[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs17239040	0.96[CEU][hapmap]
rs17239431	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17239508	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1814585	0.92[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1867641	0.92[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2278685	0.84[EUR][1000 genomes]
rs2290938	0.92[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2414491	0.96[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414492	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2414494	0.85[EUR][1000 genomes]
rs2414497	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470082	0.87[TSI][hapmap]
rs2585112	0.87[TSI][hapmap]
rs2593235	0.80[EUR][1000 genomes]
rs2593237	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2593238	0.99[EUR][1000 genomes]
rs2703580	0.89[TSI][hapmap]
rs2703593	0.88[MKK][hapmap]
rs2703596	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733170	0.87[TSI][hapmap]
rs2733332	0.87[TSI][hapmap]
rs2733341	0.82[EUR][1000 genomes]
rs2951899	0.89[TSI][hapmap]
rs2951904	0.89[TSI][hapmap]
rs2962990	0.89[TSI][hapmap]
rs2962992	0.89[TSI][hapmap]
rs3095821	0.92[CEU][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs3794613	0.88[CEU][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs4238321	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4238322	0.80[EUR][1000 genomes]
rs4303429	0.84[EUR][1000 genomes]
rs4353440	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4369592	0.84[EUR][1000 genomes]
rs4447362	0.84[EUR][1000 genomes]
rs4774250	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4774251	0.80[EUR][1000 genomes]
rs4774252	0.80[EUR][1000 genomes]
rs4774910	0.92[CEU][hapmap]
rs4774913	0.96[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4774918	0.80[EUR][1000 genomes]
rs4774919	0.80[EUR][1000 genomes]
rs5014892	0.83[EUR][1000 genomes]
rs61996955	0.81[EUR][1000 genomes]
rs62022237	0.90[EUR][1000 genomes]
rs6493901	0.92[CEU][hapmap]
rs7161965	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7175436	0.89[TSI][hapmap]
rs745652	0.96[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7496293	0.96[CEU][hapmap]
rs8033118	0.98[ASN][1000 genomes]
rs8037901	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs898901	0.87[EUR][1000 genomes]
rs935326	0.92[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs960946	0.81[EUR][1000 genomes]
rs967514	0.89[TSI][hapmap]
rs978274	0.92[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][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
rs10518899	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:57444400-57507400	Weak transcription	K562	blood
3	chr15:57451600-57491200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:57457200-57499400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
7	chr15:57459200-57492600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:57473600-57491200	Weak transcription	Gastric	stomach
9	chr15:57476200-57491200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:57477000-57492800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:57478200-57493200	Weak transcription	HepG2	liver
12	chr15:57478600-57494000	Weak transcription	Pancreas	Pancrea
13	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
14	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
16	chr15:57482400-57491200	Weak transcription	Fetal Brain Male	brain
17	chr15:57483000-57493800	Weak transcription	Colonic Mucosa	Colon
18	chr15:57484600-57493200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:57484800-57496200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:57484800-57502000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:57485000-57491200	Weak transcription	Esophagus	oesophagus
22	chr15:57485000-57501000	Weak transcription	Spleen	Spleen
23	chr15:57485000-57501800	Weak transcription	Lung	lung
24	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:57485800-57491200	Weak transcription	NHLF	lung
27	chr15:57485800-57493600	Weak transcription	A549	lung
28	chr15:57486600-57491200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:57486600-57493400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:57486600-57496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:57486800-57493000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
33	chr15:57487000-57491400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:57487000-57496600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
36	chr15:57487200-57491200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:57487200-57503000	Weak transcription	Liver	Liver
38	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:57488200-57491400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:57488400-57494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:57488400-57496000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:57488400-57496000	Weak transcription	Fetal Intestine Small	intestine
44	chr15:57488800-57491400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr15:57489200-57496000	Weak transcription	Osteobl	bone
46	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:57489400-57491400	Strong transcription	Primary T cells from cord blood	blood
48	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:57489600-57492400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:57489800-57491400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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