Variant report

Variant	rs4662219
Chromosome Location	chr2:142824137-142824138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1011862	0.89[ASN][1000 genomes]
rs10173643	0.94[ASN][1000 genomes]
rs10175827	0.83[JPT][hapmap]
rs10179841	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs10186258	0.87[ASN][1000 genomes]
rs10190170	0.84[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap]
rs10203924	0.87[ASN][1000 genomes]
rs10496912	0.85[JPT][hapmap]
rs10496913	0.89[CHB][hapmap]
rs10803487	0.80[CHB][hapmap]
rs10803489	0.87[ASN][1000 genomes]
rs10928134	0.87[CHD][hapmap]
rs11677754	0.80[ASN][1000 genomes]
rs11680286	0.81[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap]
rs11683745	0.87[ASN][1000 genomes]
rs11688838	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs11691560	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs11691595	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs12470890	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs12613064	0.92[JPT][hapmap]
rs12613097	0.92[JPT][hapmap]
rs12619411	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs13000270	0.83[ASN][1000 genomes]
rs13036224	0.80[CHB][hapmap]
rs13429550	0.82[JPT][hapmap]
rs1349219	0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1349220	0.87[ASN][1000 genomes]
rs1349221	0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1375603	0.80[ASN][1000 genomes]
rs1375606	0.89[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1375609	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1375611	0.86[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs1375613	0.86[CHD][hapmap]
rs1449475	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs1449476	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1449477	0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap]
rs1449478	0.81[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap]
rs1449480	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1449481	0.83[ASN][1000 genomes]
rs1449482	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1449489	0.81[CHB][hapmap]
rs1449490	0.81[CHB][hapmap]
rs1449498	0.80[CHB][hapmap]
rs1449499	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1449501	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1449503	0.85[CHB][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap]
rs1449504	0.81[CHB][hapmap]
rs16848074	0.92[JPT][hapmap]
rs16848107	0.92[JPT][hapmap]
rs17824487	0.80[ASN][1000 genomes]
rs17826042	0.85[JPT][hapmap]
rs1868542	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs1868543	0.80[CHB][hapmap]
rs1868544	0.81[CHB][hapmap]
rs1900933	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1900935	0.87[ASN][1000 genomes]
rs1900936	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs2029142	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs2167053	0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2197910	0.80[ASN][1000 genomes]
rs2218734	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2290140	0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap]
rs2381203	0.85[CHD][hapmap];0.91[MEX][hapmap]
rs34392492	0.80[ASN][1000 genomes]
rs4550611	0.84[ASN][1000 genomes]
rs4662370	0.87[CHD][hapmap]
rs4662373	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4662389	0.89[ASN][1000 genomes]
rs4662396	0.81[EUR][1000 genomes]
rs6712994	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6744928	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754907	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs736602	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs7558803	0.82[CHD][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs7565655	0.87[ASN][1000 genomes]
rs7566250	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7581031	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs7586417	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7598886	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs7605112	0.81[CHB][hapmap]
rs7608258	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7609479	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs9287332	0.87[ASN][1000 genomes]
rs957376	0.81[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap]
rs970600	0.85[JPT][hapmap]
rs970601	0.85[JPT][hapmap]
rs9941495	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs997123	0.82[ASN][1000 genomes]
rs9973706	0.93[JPT][hapmap];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	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875253	chr2:142805006-142855291	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4662219	NXPH2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142821800-142824600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:142823000-142824400	Weak transcription	Brain Anterior Caudate	brain

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