Variant report

Variant	rs12904634
Chromosome Location	chr15:57539366-57539367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1037956	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs10518894	0.86[ASW][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10518895	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10518899	0.88[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs11071309	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11631541	1.00[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs11632069	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11635440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11637955	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11852340	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11853331	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11855648	0.86[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11857507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11858783	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12050751	0.92[CEU][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs12898327	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12899036	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12900589	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12900874	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12904602	0.85[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs12904933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12906042	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12910094	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12912210	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs12912868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12914425	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12915489	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs12917247	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13313455	0.91[JPT][hapmap]
rs1462156	0.92[CEU][hapmap]
rs1545728	0.88[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs16977374	0.84[MKK][hapmap]
rs17239508	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1814585	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs1867641	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs2169466	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2290938	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap]
rs2414491	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2414492	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2464429	0.95[JPT][hapmap]
rs2464430	0.95[JPT][hapmap]
rs2585112	0.91[JPT][hapmap]
rs2615231	0.91[JPT][hapmap]
rs2703576	0.90[JPT][hapmap]
rs2703580	0.95[JPT][hapmap];0.80[TSI][hapmap]
rs2733188	0.91[JPT][hapmap]
rs2733332	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2920267	0.95[JPT][hapmap]
rs2951899	0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2951903	0.91[JPT][hapmap]
rs2951904	0.91[JPT][hapmap];0.80[TSI][hapmap]
rs2962990	0.95[JPT][hapmap];0.80[TSI][hapmap]
rs2962991	0.95[JPT][hapmap]
rs2962992	0.90[JPT][hapmap]
rs2962993	0.91[JPT][hapmap]
rs3095821	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs3794613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap]
rs4238321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4353440	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4774250	0.85[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4774910	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4774913	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6493901	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7161965	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7175436	0.91[JPT][hapmap]
rs745652	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs8024901	0.84[MKK][hapmap]
rs8037901	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs935326	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs967514	0.91[JPT][hapmap];0.80[TSI][hapmap]
rs978274	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv974581	chr15:57538491-57540100	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1541234	chr15:57539363-57539366	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
4	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
7	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
8	chr15:57524400-57540600	Strong transcription	Primary T cells from cord blood	blood
9	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
10	chr15:57526000-57542600	Weak transcription	Right Ventricle	heart
11	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
15	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:57528200-57545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:57528400-57554800	Weak transcription	NHEK	skin
20	chr15:57529000-57545400	Weak transcription	HMEC	breast
21	chr15:57529400-57543400	Weak transcription	HUVEC	blood vessel
22	chr15:57529600-57540000	Weak transcription	Fetal Heart	heart
23	chr15:57530200-57543400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:57531000-57542400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:57531400-57541200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:57531600-57540200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:57535000-57539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:57535000-57540000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:57535000-57541200	Strong transcription	NH-A	brain
32	chr15:57535200-57540000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:57535200-57542600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:57535400-57540000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:57535400-57540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:57535600-57539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:57535600-57539600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:57535600-57539800	Strong transcription	Adipose Nuclei	Adipose
39	chr15:57535600-57540200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:57535600-57540200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:57535600-57540200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:57535600-57540400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:57535600-57540400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:57535600-57540600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:57535600-57541400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:57535600-57541800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:57535800-57540000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:57535800-57540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:57536000-57540600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:57536000-57540600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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