Variant report

Variant	rs1438040
Chromosome Location	chr2:178640880-178640881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10166758	0.92[YRI][hapmap]
rs10178473	0.93[ASN][1000 genomes]
rs10178858	0.93[ASN][1000 genomes]
rs10178916	0.93[ASN][1000 genomes]
rs10179500	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10182017	0.94[ASN][1000 genomes]
rs10182353	0.92[ASN][1000 genomes]
rs10185318	0.91[ASN][1000 genomes]
rs10202536	0.88[ASN][1000 genomes]
rs10930814	0.91[MEX][hapmap]
rs13389387	0.84[ASN][1000 genomes]
rs13395965	0.96[ASN][1000 genomes]
rs13396065	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13396537	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13421315	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs13421345	0.96[ASN][1000 genomes]
rs13421415	0.84[ASN][1000 genomes]
rs1344923	0.81[CHD][hapmap]
rs1438042	0.96[ASN][1000 genomes]
rs1438060	0.81[JPT][hapmap]
rs1438062	0.81[JPT][hapmap]
rs1530035	0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1530036	0.87[ASN][1000 genomes]
rs1880915	0.91[MEX][hapmap]
rs1898585	0.87[ASN][1000 genomes]
rs2033763	0.91[YRI][hapmap]
rs2037757	0.92[MEX][hapmap]
rs2365895	0.81[JPT][hapmap]
rs2695112	0.83[MEX][hapmap]
rs2695735	0.83[MEX][hapmap]
rs28380215	0.92[ASN][1000 genomes]
rs2886499	0.81[JPT][hapmap]
rs2886500	0.81[JPT][hapmap]
rs3754996	0.85[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3770036	0.82[ASN][1000 genomes]
rs3770044	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3770045	0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3770048	0.81[JPT][hapmap]
rs3770051	0.85[TSI][hapmap]
rs3821010	0.81[JPT][hapmap]
rs41440047	0.81[JPT][hapmap]
rs4297923	0.94[ASN][1000 genomes]
rs4413189	0.81[JPT][hapmap]
rs4446096	0.81[JPT][hapmap]
rs4464321	0.92[ASN][1000 genomes]
rs4487116	0.84[ASN][1000 genomes]
rs4522644	0.81[JPT][hapmap]
rs56314683	0.96[ASN][1000 genomes]
rs56690966	0.96[ASN][1000 genomes]
rs56760518	0.82[ASN][1000 genomes]
rs57342997	0.96[ASN][1000 genomes]
rs62183048	0.83[ASN][1000 genomes]
rs62183050	0.83[ASN][1000 genomes]
rs6433694	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6433698	0.81[JPT][hapmap]
rs6705118	0.80[JPT][hapmap]
rs6706739	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6708580	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709966	0.96[ASN][1000 genomes]
rs6714147	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6718100	0.95[ASN][1000 genomes]
rs6718657	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6718860	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6718993	0.96[ASN][1000 genomes]
rs6720891	0.81[JPT][hapmap]
rs6726253	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6726502	0.96[ASN][1000 genomes]
rs6733980	0.94[ASN][1000 genomes]
rs6735387	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6737872	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6743821	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6751656	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6752264	0.96[ASN][1000 genomes]
rs6758508	0.96[ASN][1000 genomes]
rs6758543	0.84[JPT][hapmap]
rs7557283	0.80[JPT][hapmap]
rs7563242	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7568068	0.81[JPT][hapmap]
rs7570898	0.80[JPT][hapmap]
rs7581861	0.81[JPT][hapmap]
rs7584946	0.83[ASN][1000 genomes]
rs7605091	0.84[ASN][1000 genomes]
rs934802	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1438040	SP3	cis	parietal	SCAN
rs1438040	TTC30A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178638000-178647600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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