Variant report

Variant	rs3853119
Chromosome Location	chr5:14647108-14647109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13189930	0.80[JPT][hapmap]
rs149493	0.87[ASN][1000 genomes]
rs149617	0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs152788	0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs153829	0.84[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs153830	0.82[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs166127	0.83[ASN][1000 genomes]
rs1875513	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.94[ASN][1000 genomes]
rs2455402	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs250439	0.87[ASN][1000 genomes]
rs250440	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs250862	0.83[ASN][1000 genomes]
rs251496	0.84[ASN][1000 genomes]
rs258290	0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs258374	0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs25945	0.93[JPT][hapmap]
rs25951	0.93[JPT][hapmap]
rs25952	0.93[JPT][hapmap]
rs25983	0.80[JPT][hapmap]
rs25986	0.86[JPT][hapmap]
rs25987	0.86[JPT][hapmap]
rs25988	0.86[JPT][hapmap]
rs25992	0.86[JPT][hapmap]
rs26307	0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs27356	0.80[JPT][hapmap]
rs27911	0.86[JPT][hapmap]
rs28004	0.93[JPT][hapmap]
rs31920	0.93[JPT][hapmap]
rs31922	0.84[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs31923	0.93[JPT][hapmap]
rs31925	0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs31926	0.93[JPT][hapmap]
rs31928	0.92[JPT][hapmap]
rs31929	0.93[JPT][hapmap]
rs31930	0.86[JPT][hapmap]
rs31968	0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3866215	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs42358	0.93[JPT][hapmap]
rs42681	0.91[JPT][hapmap]
rs456180	0.84[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap]
rs466880	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs4702043	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6554855	0.81[ASN][1000 genomes]
rs6554856	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs6872954	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs745328	0.85[JPT][hapmap]
rs95492	0.86[JPT][hapmap]

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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv830211	chr5:14474675-14675776	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1032951	chr5:14529579-14667342	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3450688	chr5:14647077-14649300	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3853119	PSMD7	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14646200-14648600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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