Variant report

Variant	rs6782253
Chromosome Location	chr3:119402443-119402444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119397978..119400630-chr3:119401218..119403216,2	MCF-7	breast:
2	chr3:118876250..118878600-chr3:119400821..119403241,2	MCF-7	breast:
3	chr3:119394872..119397577-chr3:119400469..119404472,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11720605	0.83[EUR][1000 genomes]
rs13062540	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065893	0.92[ASN][1000 genomes]
rs1317259	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880040	0.94[ASN][1000 genomes]
rs1880041	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2046430	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629395	0.91[ASN][1000 genomes]
rs2629397	0.83[EUR][1000 genomes]
rs2629409	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670296	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688633	0.82[EUR][1000 genomes]
rs2698282	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749416	0.92[ASN][1000 genomes]
rs3749417	0.92[ASN][1000 genomes]
rs3772134	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4327424	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687871	0.93[ASN][1000 genomes]
rs4688023	0.94[ASN][1000 genomes]
rs484809	0.88[ASN][1000 genomes]
rs523476	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552244	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571352	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62265884	0.83[EUR][1000 genomes]
rs6438541	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438542	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785698	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794484	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6794579	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807079	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs693397	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613999	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633444	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007	0.88[ASN][1000 genomes]
rs940181	0.83[EUR][1000 genomes]

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	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6782253	POPDC2	cis	lung	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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