Variant report

Variant	rs409190
Chromosome Location	chr4:172893271-172893272
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11722467	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12503009	0.97[EUR][1000 genomes]
rs12503041	0.97[EUR][1000 genomes]
rs12510139	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs12510280	0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs13118856	0.86[EUR][1000 genomes]
rs13145737	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13152268	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1485872	0.92[CEU][hapmap]
rs17057754	0.96[CEU][hapmap]
rs17057759	0.88[CEU][hapmap]
rs179639	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs189144	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs230	0.84[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2332433	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2332434	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2877676	0.88[EUR][1000 genomes]
rs3113678	0.96[CEU][hapmap]
rs332962	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs332965	1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs332966	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs332967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332969	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs332971	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap]
rs332979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333003	0.88[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs333004	0.81[CEU][hapmap]
rs373772	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs392614	0.92[CEU][hapmap]
rs405831	0.92[CEU][hapmap]
rs405986	0.96[CEU][hapmap]
rs408196	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs414428	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs420648	0.96[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4505786	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs453429	0.96[CEU][hapmap]
rs4692907	0.96[CEU][hapmap]
rs547753	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs578496	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62326334	0.96[EUR][1000 genomes]
rs62326336	0.96[EUR][1000 genomes]
rs6832654	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs693756	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7434835	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs9993396	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1022527	chr4:172547732-173236939	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537357	chr4:172547732-173236939	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1024693	chr4:172609237-173236939	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv520744	chr4:172797761-172897603	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv498033	chr4:172830955-173121438	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1025388	chr4:172891427-172951140	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs409190	GALNTL6	cis	parietal	SCAN
rs409190	LOC646870	trans	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