Variant report

Variant	rs1438062
Chromosome Location	chr2:178695730-178695731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10169917	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179500	0.81[JPT][hapmap]
rs10182386	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10930809	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10930811	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11687117	0.84[CEU][hapmap]
rs11884289	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13384016	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13396065	0.81[JPT][hapmap]
rs13396537	0.81[JPT][hapmap]
rs13409414	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13424417	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs1344922	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1438040	0.81[JPT][hapmap]
rs1438053	0.84[CEU][hapmap]
rs1438060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1438063	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1852503	0.84[CEU][hapmap]
rs1946813	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1946814	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs2365895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2365896	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2365897	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695115	0.84[CEU][hapmap]
rs2695730	0.83[CEU][hapmap]
rs2695757	0.84[CEU][hapmap]
rs2886499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2886500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770048	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs41440047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4324348	0.84[CEU][hapmap]
rs4413189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4446096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4522644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6433694	0.81[JPT][hapmap]
rs6433697	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6705472	0.84[CEU][hapmap]
rs6710818	0.86[EUR][1000 genomes]
rs6713981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714147	0.81[JPT][hapmap]
rs6714519	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6718657	0.81[JPT][hapmap]
rs6718860	0.81[JPT][hapmap]
rs6720891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs6726253	0.81[JPT][hapmap]
rs6729216	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6729482	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6736927	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs6737872	0.81[JPT][hapmap]
rs6739044	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6743821	0.81[JPT][hapmap]
rs6751656	0.81[JPT][hapmap]
rs6758473	0.88[CEU][hapmap]
rs6758543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7557283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7568068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7570898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7581861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7595951	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs934800	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs934801	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs934802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.91[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583690	chr2:178638381-178712283	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv3053	chr2:178690640-178735132	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1438062	FKBP7	cis	parietal	SCAN
rs1438062	SESTD1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178693600-178695800	Weak transcription	Adipose Nuclei	Adipose
2	chr2:178694000-178696200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:178694800-178696400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:178695600-178696400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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