Variant report

Variant	rs11631541
Chromosome Location	chr15:57361676-57361677
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57355187..57357416-chr15:57359141..57362013,2	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1037956	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs10518894	0.86[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.80[TSI][hapmap]
rs10518895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518899	0.89[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11071305	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11071309	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11630195	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11631228	0.90[AMR][1000 genomes]
rs11632069	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11637955	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11852340	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap]
rs11853331	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs11855648	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap]
rs11857507	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11858471	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11858783	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12050751	0.85[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs12898327	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]
rs12898844	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899036	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12899187	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12899915	0.85[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900589	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12900874	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12900986	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12901780	0.88[AMR][1000 genomes]
rs12903578	0.83[AMR][1000 genomes]
rs12904602	0.85[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs12904634	1.00[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs12904933	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12905900	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906042	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12906873	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12906936	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12908670	0.83[AMR][1000 genomes]
rs12909811	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910094	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12910132	0.86[MKK][hapmap]
rs12912210	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs12912868	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12914182	0.84[AMR][1000 genomes]
rs12914410	0.83[AMR][1000 genomes]
rs12914425	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12915473	0.82[AMR][1000 genomes]
rs12915489	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12916237	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12916958	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12917247	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313455	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1430823	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1462156	0.85[CEU][hapmap]
rs1545728	0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1628067	0.85[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs17239040	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17239452	0.86[MKK][hapmap]
rs17239508	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17819700	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1814585	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs1820995	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1867641	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2053472	0.83[AMR][1000 genomes]
rs2111891	0.87[AMR][1000 genomes]
rs2116065	0.90[AMR][1000 genomes]
rs2116066	0.90[AMR][1000 genomes]
rs213149	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs213164	0.83[AMR][1000 genomes]
rs2169466	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2290938	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs2414490	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2414491	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs2414492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2414494	0.84[AMR][1000 genomes]
rs2435907	0.81[ASN][1000 genomes]
rs2439918	0.82[ASN][1000 genomes]
rs2464429	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2464430	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2470079	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2470082	0.80[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs2583108	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2585082	0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2585087	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2585088	0.80[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2585102	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2585112	0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs2615231	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2703576	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2703577	0.84[ASN][1000 genomes]
rs2703580	0.95[JPT][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs2733170	0.80[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs2733171	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2733174	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2733176	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733177	0.82[ASN][1000 genomes]
rs2733181	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2733182	0.82[ASN][1000 genomes]
rs2733185	0.84[ASN][1000 genomes]
rs2733188	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2733332	0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2920267	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2920269	0.88[ASN][1000 genomes]
rs2951895	0.83[ASN][1000 genomes]
rs2951899	0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2951901	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2951903	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2951904	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs2962990	0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs2962991	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2962992	0.90[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs2962993	0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34262415	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes]
rs35646942	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3794613	1.00[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs3803454	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs3803455	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4238321	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4353440	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4774250	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4774898	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4774899	0.85[AMR][1000 genomes]
rs4774902	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4774910	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4774913	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap]
rs62022986	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62022988	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62025331	0.85[AMR][1000 genomes]
rs6493901	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs715338	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs7161965	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7175436	0.80[CHB][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]
rs745652	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs7496293	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8037901	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs967514	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs978274	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][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
rs11631541	PRTG	cis	parietal	SCAN

Chromatin state (count:78 , 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	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
5	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
6	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
8	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
10	chr15:57348200-57361800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:57349800-57363800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
13	chr15:57350200-57363800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:57350400-57362400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
16	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr15:57350400-57374000	Weak transcription	Ovary	ovary
18	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:57353200-57362800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:57353400-57362600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:57353400-57371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:57353600-57362400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:57353600-57364200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:57353800-57362000	Weak transcription	HepG2	liver
25	chr15:57353800-57363800	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:57353800-57364800	Weak transcription	HSMM	muscle
27	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
28	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:57354200-57361800	Weak transcription	NHDF-Ad	bronchial
30	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:57354600-57371600	Weak transcription	NH-A	brain
32	chr15:57355000-57374000	Weak transcription	Osteobl	bone
33	chr15:57355400-57365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
35	chr15:57356400-57364400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:57356400-57370800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:57356400-57371000	Weak transcription	Dnd41	blood
38	chr15:57356400-57371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:57356600-57364800	Weak transcription	Fetal Kidney	kidney
41	chr15:57356600-57372000	Weak transcription	Primary B cells from cord blood	blood
42	chr15:57356800-57362200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:57356800-57371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:57357400-57362800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr15:57357600-57362600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:57357600-57366600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr15:57357600-57371600	Weak transcription	HUVEC	blood vessel
48	chr15:57358400-57362000	Weak transcription	Brain Angular Gyrus	brain
49	chr15:57359200-57362200	Enhancers	HMEC	breast
50	chr15:57359800-57363000	Enhancers	A549	lung

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