Variant report

Variant	rs16969786
Chromosome Location	chr15:40039555-40039556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR176-2	chr15:40039503-40039648	NONHSAT041767

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1166717	0.83[ASN][1000 genomes]
rs1166721	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12439384	0.87[ASN][1000 genomes]
rs12591862	1.00[JPT][hapmap]
rs12594027	0.83[ASN][1000 genomes]
rs12595664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1491625	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1602543	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1906162	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1906163	0.83[ASN][1000 genomes]
rs1906164	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs1906165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638012	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60676466	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492916	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67248221	0.89[ASN][1000 genomes]
rs67895637	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168010	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7169027	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72727074	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72727076	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028323	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036018	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][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	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40029200-40040200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:40033600-40040200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:40035000-40040400	Weak transcription	Adipose Nuclei	Adipose
4	chr15:40035600-40050000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40037000-40039600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr15:40037800-40041400	Enhancers	Hela-S3	cervix
7	chr15:40038000-40040400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:40038200-40039600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:40038400-40039600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:40038400-40040800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:40038400-40041200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:40038400-40041200	Enhancers	Osteobl	bone
13	chr15:40038600-40040200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:40038600-40041200	Enhancers	NHDF-Ad	bronchial
15	chr15:40039000-40040200	Enhancers	A549	lung
16	chr15:40039200-40039600	Enhancers	NH-A	brain
17	chr15:40039200-40041000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr15:40039400-40039800	Enhancers	HMEC	breast
19	chr15:40039400-40040800	Enhancers	NHEK	skin
20	chr15:40039400-40049000	Weak transcription	HUVEC	blood vessel

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