Variant report

Variant	rs4389093
Chromosome Location	chr15:49743069-49743070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10519224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519225	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851478	1.00[YRI][hapmap]
rs10851479	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs11070695	0.83[ASN][1000 genomes]
rs11070699	0.82[JPT][hapmap]
rs11070706	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11852336	0.80[ASN][1000 genomes]
rs11853248	0.88[ASN][1000 genomes]
rs11853969	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs11854557	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs11854671	0.87[ASN][1000 genomes]
rs11855798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857515	1.00[YRI][hapmap]
rs11858411	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12050614	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12148764	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12232355	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12591300	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591317	0.80[ASN][1000 genomes]
rs12591659	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12592508	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12593151	0.90[ASN][1000 genomes]
rs12595692	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12901929	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902096	0.80[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs12902271	1.00[YRI][hapmap]
rs12902960	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs12905203	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905477	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap]
rs12906972	0.87[ASN][1000 genomes]
rs12907661	0.81[ASN][1000 genomes]
rs12907918	0.86[ASN][1000 genomes]
rs12907944	0.87[ASN][1000 genomes]
rs12908624	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12908635	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12912703	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12916839	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395901	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1395903	0.87[ASN][1000 genomes]
rs17402115	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17478694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479589	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1874616	0.82[JPT][hapmap]
rs1911612	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1976551	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2202714	0.82[JPT][hapmap]
rs2413956	0.87[ASN][1000 genomes]
rs2899434	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34002493	0.90[ASN][1000 genomes]
rs34146550	0.81[ASN][1000 genomes]
rs34246470	0.87[ASN][1000 genomes]
rs34414487	0.87[ASN][1000 genomes]
rs34694913	0.87[ASN][1000 genomes]
rs35698479	0.85[ASN][1000 genomes]
rs36023246	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4436732	0.90[ASN][1000 genomes]
rs4480740	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4547278	0.90[ASN][1000 genomes]
rs4775806	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs4775816	0.87[ASN][1000 genomes]
rs55904469	0.87[ASN][1000 genomes]
rs62009977	0.90[ASN][1000 genomes]
rs62021589	0.86[ASN][1000 genomes]
rs62022665	0.86[ASN][1000 genomes]
rs62022667	0.87[ASN][1000 genomes]
rs6493372	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs7162741	0.86[ASN][1000 genomes]
rs7172906	0.85[ASN][1000 genomes]
rs7174135	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7180168	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs753857	0.82[JPT][hapmap]
rs8032688	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs925104	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs9920722	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv526246	chr15:49738233-49749735	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4389093	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49730400-49744600	Weak transcription	NHLF	lung
2	chr15:49732000-49750200	Weak transcription	HSMM	muscle
3	chr15:49737000-49751200	Weak transcription	Ovary	ovary
4	chr15:49737600-49744200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:49739200-49744200	Weak transcription	NHDF-Ad	bronchial
6	chr15:49741000-49743200	Enhancers	Rectal Smooth Muscle	rectum
7	chr15:49741200-49743200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:49741600-49743200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:49741800-49747400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:49742000-49752000	Weak transcription	Adipose Nuclei	Adipose
11	chr15:49742200-49743200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:49742800-49748000	Weak transcription	Fetal Heart	heart
13	chr15:49742800-49750400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:49743000-49744600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:49743000-49744600	Weak transcription	Osteobl	bone
16	chr15:49743000-49745600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:49743000-49748000	Weak transcription	Fetal Lung	lung

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