Variant report

Variant	rs225620
Chromosome Location	chr6:142464888-142464889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142461332..142463254-chr6:142463740..142465294,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11758623	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs178783	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs225601	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225602	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225604	1.00[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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs225605	0.93[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs225606	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225618	0.93[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225622	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225624	1.00[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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225628	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225630	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225631	0.93[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225632	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225633	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225634	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225635	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225636	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225639	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225640	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225641	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225642	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225643	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225648	0.81[TSI][hapmap]
rs225650	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225651	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225652	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225653	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225654	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225655	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225656	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225657	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225658	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225659	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225660	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225661	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225662	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225663	0.87[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225664	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225665	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225666	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225667	0.81[ASN][1000 genomes]
rs225668	0.81[ASN][1000 genomes]
rs225670	0.81[ASN][1000 genomes]
rs225671	0.81[ASW][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs225672	0.81[ASN][1000 genomes]
rs225673	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225674	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225675	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225676	0.81[ASW][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[ASN][1000 genomes]
rs225677	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225678	1.00[JPT][hapmap]
rs225679	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225684	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs225685	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225687	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs225689	1.00[JPT][hapmap]
rs225695	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225700	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225701	1.00[JPT][hapmap]
rs225702	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225710	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs4896574	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4896575	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs56185739	0.81[ASN][1000 genomes]
rs62430473	0.82[ASN][1000 genomes]
rs628311	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs639658	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6939944	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939975	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.81[JPT][hapmap]
rs9389979	0.81[JPT][hapmap]
rs9389980	0.81[JPT][hapmap]

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	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886735	chr6:142365171-142472294	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs225620	VTA1	cis	parietal	SCAN

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

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links