Variant report

Variant	rs940181
Chromosome Location	chr3:119413071-119413072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11720605	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062540	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs13065543	0.83[GIH][hapmap]
rs1317259	0.81[EUR][1000 genomes]
rs1880041	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2046430	0.88[EUR][1000 genomes]
rs2629395	0.83[GIH][hapmap]
rs2629397	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2629409	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2670296	0.88[EUR][1000 genomes]
rs2688633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692618	0.80[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs2698282	0.88[EUR][1000 genomes]
rs3772134	0.92[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4327424	0.92[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs484809	0.81[GIH][hapmap]
rs523476	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs552244	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs571352	0.92[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs62265884	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438541	0.81[EUR][1000 genomes]
rs6438542	0.92[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs6766563	0.90[JPT][hapmap]
rs6782253	0.83[EUR][1000 genomes]
rs6785698	0.93[EUR][1000 genomes]
rs6794484	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6794579	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6807079	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs693397	0.88[EUR][1000 genomes]
rs7613999	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7626940	0.90[JPT][hapmap]
rs7633444	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs8007	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3358659	chr3:119402929-119414857	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv591391	chr3:119403145-119442572	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs940181	POPDC2	cis	multi-tissue	Pritchard
rs940181	POPDC2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119406000-119421400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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