Variant report

Variant	rs4547278
Chromosome Location	chr15:49781725-49781726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10519224	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10519225	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10851479	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070695	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11637582	0.86[ASN][1000 genomes]
rs11852336	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853248	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853969	0.84[AFR][1000 genomes]
rs11854557	0.84[AFR][1000 genomes]
rs11854671	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855798	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11857515	0.80[AFR][1000 genomes]
rs11858411	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050614	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050624	0.86[ASN][1000 genomes]
rs12148764	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12232355	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591300	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12591317	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12591659	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12593151	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595692	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901680	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901929	0.84[AFR][1000 genomes]
rs12902096	0.84[AFR][1000 genomes]
rs12902960	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905477	0.84[AFR][1000 genomes]
rs12906134	0.90[ASN][1000 genomes]
rs12906972	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907661	0.91[ASN][1000 genomes]
rs12907918	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907944	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908624	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908635	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912703	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916839	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1395901	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1395903	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17478694	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17478785	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17479589	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911612	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948975	0.87[ASN][1000 genomes]
rs1961393	0.84[AFR][1000 genomes]
rs1976551	0.91[ASN][1000 genomes]
rs2413956	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899434	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34002493	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34146550	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34246470	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34414487	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34694913	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34941109	0.87[ASN][1000 genomes]
rs35698479	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36023246	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs36100631	0.84[AFR][1000 genomes]
rs4389093	0.90[ASN][1000 genomes]
rs4436732	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480740	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774538	0.84[AFR][1000 genomes]
rs4775806	0.84[AFR][1000 genomes]
rs4775808	0.88[AFR][1000 genomes]
rs4775816	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55904469	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55979115	0.84[AFR][1000 genomes]
rs62009834	0.84[AFR][1000 genomes]
rs62009977	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62021589	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022665	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022667	0.97[ASN][1000 genomes]
rs6493372	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162741	0.96[ASN][1000 genomes]
rs7172906	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7174135	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180168	0.84[AFR][1000 genomes]
rs8032688	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033476	0.86[ASN][1000 genomes]
rs925104	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1043119	chr15:49760222-49844366	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv13246	chr15:49767876-49782252	Genic enhancers Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
5	nsv984069	chr15:49772310-49783159	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4547278	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49764600-49788400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:49765800-49783200	Weak transcription	NHDF-Ad	bronchial
3	chr15:49775200-49781800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:49777200-49788800	Weak transcription	Fetal Lung	lung
5	chr15:49778400-49787200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:49780000-49781800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:49781000-49781800	Strong transcription	Osteobl	bone
8	chr15:49781600-49781800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links