Variant report

Variant	rs62260715
Chromosome Location	chr3:49829326-49829327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49822569..49826385-chr3:49827149..49830694,4	MCF-7	breast:
2	chr3:49823360..49825533-chr3:49829007..49831424,3	K562	blood:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049413	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1049256	0.94[ASN][1000 genomes]
rs10865958	0.89[ASN][1000 genomes]
rs10865959	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130214	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130216	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130218	0.92[ASN][1000 genomes]
rs11130219	0.92[ASN][1000 genomes]
rs11130221	0.94[ASN][1000 genomes]
rs1128535	0.89[ASN][1000 genomes]
rs11709680	0.92[ASN][1000 genomes]
rs11710675	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714957	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715304	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11716575	0.92[ASN][1000 genomes]
rs11717256	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717463	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11920900	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12381242	0.92[ASN][1000 genomes]
rs12490656	0.89[ASN][1000 genomes]
rs12496226	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13063621	0.94[ASN][1000 genomes]
rs13084243	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13085679	0.89[ASN][1000 genomes]
rs13086130	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13086465	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13090611	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317140	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316065	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491986	0.92[ASN][1000 genomes]
rs1799843	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799845	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234385	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234391	0.92[ASN][1000 genomes]
rs2246832	0.87[ASN][1000 genomes]
rs2247036	0.87[ASN][1000 genomes]
rs2271960	0.87[ASN][1000 genomes]
rs2271961	0.87[ASN][1000 genomes]
rs2276864	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291542	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2307021	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2352967	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352974	0.87[ASN][1000 genomes]
rs2352975	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34451146	0.94[ASN][1000 genomes]
rs34522271	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34614773	0.92[ASN][1000 genomes]
rs34735338	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35210174	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35261599	0.96[ASN][1000 genomes]
rs35474403	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749237	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749240	0.94[ASN][1000 genomes]
rs3749241	0.94[ASN][1000 genomes]
rs3811695	0.90[ASN][1000 genomes]
rs3811696	0.92[ASN][1000 genomes]
rs3819325	0.84[ASN][1000 genomes]
rs4519692	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855841	0.89[ASN][1000 genomes]
rs4855850	0.92[ASN][1000 genomes]
rs4855862	0.92[ASN][1000 genomes]
rs4855867	0.92[ASN][1000 genomes]
rs57648519	0.94[ASN][1000 genomes]
rs59906301	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60205400	0.94[ASN][1000 genomes]
rs62260719	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260729	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446295	0.96[ASN][1000 genomes]
rs6766836	0.94[ASN][1000 genomes]
rs6775384	0.89[ASN][1000 genomes]
rs6785549	0.89[ASN][1000 genomes]
rs6802890	0.96[ASN][1000 genomes]
rs6804655	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs695238	0.89[ASN][1000 genomes]
rs71324996	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7372725	0.88[ASN][1000 genomes]
rs7372730	0.90[ASN][1000 genomes]
rs7372966	0.88[ASN][1000 genomes]
rs7374183	0.88[ASN][1000 genomes]
rs7374277	0.88[ASN][1000 genomes]
rs7429353	0.88[ASN][1000 genomes]
rs7431078	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431106	0.94[ASN][1000 genomes]
rs7618501	0.95[ASN][1000 genomes]
rs7618519	0.96[ASN][1000 genomes]
rs7629936	0.94[ASN][1000 genomes]
rs7634886	0.92[ASN][1000 genomes]
rs7634902	0.94[ASN][1000 genomes]
rs7645061	0.89[ASN][1000 genomes]
rs7648987	0.89[ASN][1000 genomes]
rs7649348	0.96[ASN][1000 genomes]
rs9814765	0.92[ASN][1000 genomes]
rs9815766	0.94[ASN][1000 genomes]
rs9819511	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850465	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9853458	0.92[ASN][1000 genomes]
rs9855505	0.88[ASN][1000 genomes]
rs9859153	0.94[ASN][1000 genomes]
rs9865480	0.92[ASN][1000 genomes]
rs9871654	0.95[ASN][1000 genomes]
rs9872864	0.88[ASN][1000 genomes]
rs9873183	0.87[ASN][1000 genomes]
rs9876508	0.96[ASN][1000 genomes]
rs9882639	0.94[ASN][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62260715	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs62260715	BSN-AS2	cis	Muscle Skeletal	GTEx
rs62260715	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49824600-49832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49824800-49832600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49825200-49836400	Weak transcription	Esophagus	oesophagus
4	chr3:49825600-49840000	Weak transcription	Spleen	Spleen
5	chr3:49827400-49829600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:49828200-49829400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:49828400-49832600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:49829200-49832800	Weak transcription	Placenta Amnion	Placenta Amnion

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