Variant report

Variant	rs11070275
Chromosome Location	chr15:40791115-40791116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40789702..40793899-chr15:40802454..40805435,6	K562	blood:
2	chr15:40789021..40791161-chr15:40792541..40794393,2	K562	blood:
3	chr15:40790726..40793810-chr15:40802454..40804415,3	K562	blood:
4	chr15:40788119..40791373-chr15:40792541..40795559,4	K562	blood:
5	chr15:40761859..40764280-chr15:40788423..40791384,2	MCF-7	breast:
6	chr15:40782898..40785879-chr15:40789263..40792027,2	K562	blood:

Variant related genes	Relation type
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11070277	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070285	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs11070286	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap]
rs11632061	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11632370	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11638742	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639464	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852694	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs11854986	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs11855334	0.96[CEU][hapmap];0.83[CHD][hapmap];0.81[TSI][hapmap]
rs11855923	0.96[CEU][hapmap]
rs11856438	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs11856802	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs11858113	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs12594548	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12595610	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12905162	0.96[CEU][hapmap]
rs12914743	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs12916042	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916323	0.80[CEU][hapmap]
rs16970851	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs1806961	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1811513	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1813898	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1869301	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1869302	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1993212	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2034651	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2034652	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2167795	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412531	0.86[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2412532	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2412534	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2412544	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs2444302	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2924386	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2924388	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959536	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2959545	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3092979	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs35047458	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs3751653	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs4923875	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4923876	0.86[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4924472	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924478	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924479	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924480	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924481	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs588686	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590046	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs603623	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs616937	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618399	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs619711	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs620198	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492947	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs6492951	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs654317	0.84[EUR][1000 genomes]
rs6582	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7178756	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7183273	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7494968	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026605	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs8029384	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs8034326	0.82[EUR][1000 genomes]
rs8041534	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs896795	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9652415	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976401	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs11070275	C15orf57	cis	Esophagus Muscularis	GTEx
rs11070275	C15orf57	cis	lymphoblastoid	seeQTL
rs11070275	CCDC32	cis	lesional skin	skin_eQTL
rs11070275	RP11-111A22.1	cis	lung	GTEx
rs11070275	ITPKA	cis	parietal	SCAN
rs11070275	ZFYVE19	cis	cerebellum	SCAN
rs11070275	CCDC32	cis	normal skin	skin_eQTL
rs11070275	C15orf57	cis	Nerve Tibial	GTEx
rs11070275	C15orf57	cis	Artery Tibial	GTEx
rs11070275	DISP2	cis	parietal	SCAN
rs11070275	RP11-111A22.1	cis	Artery Aorta	GTEx
rs11070275	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs11070275	C15orf23	cis	cerebellum	SCAN
rs11070275	C15orf57	cis	lung	GTEx
rs11070275	C15orf57	cis	Heart Left Ventricle	GTEx
rs11070275	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs11070275	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs11070275	C15orf57	cis	Lymphoblastoid	GTEx
rs11070275	PLA2G4E	cis	parietal	SCAN
rs11070275	IVD	cis	cerebellum	SCAN
rs11070275	CCDC32	cis	multi-tissue	Pritchard
rs11070275	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs11070275	C15orf57	cis	Artery Aorta	GTEx
rs11070275	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs11070275	C15orf57	cis	Cerebellum	GTEx
rs11070275	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11070275	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs11070275	LPCAT4	cis	parietal	SCAN
rs11070275	C15orf57	cis	parietal	SCAN
rs11070275	C15orf57	cis	cerebellum	SCAN
rs11070275	C15orf57	cis	Muscle Skeletal	GTEx
rs11070275	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40786200-40791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:40786200-40792400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:40786400-40791400	Weak transcription	Hela-S3	cervix
4	chr15:40786600-40792800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:40786600-40799200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:40790400-40791200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:40790400-40791400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:40790400-40791400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:40790400-40791400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:40790400-40791600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:40790600-40791200	Enhancers	HSMMtube	muscle
12	chr15:40790600-40791400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:40791000-40791200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:40791000-40791200	Flanking Active TSS	NH-A	brain
15	chr15:40791000-40791200	Flanking Active TSS	Osteobl	bone
16	chr15:40791000-40791600	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links