Variant report

Variant	rs179641
Chromosome Location	chr4:172866682-172866683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10031122	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10866351	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11931247	1.00[CEU][hapmap];0.91[MEX][hapmap];0.87[EUR][1000 genomes]
rs13106824	1.00[CEU][hapmap]
rs13111782	0.87[EUR][1000 genomes]
rs13130415	0.82[CEU][hapmap]
rs1385794	0.88[EUR][1000 genomes]
rs1485863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1485867	0.82[CEU][hapmap]
rs189146	0.94[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs332980	0.88[EUR][1000 genomes]
rs332982	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs332983	1.00[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs332992	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs332993	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap]
rs332995	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs332996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs333002	0.93[CEU][hapmap]
rs6553603	0.94[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs6818985	0.82[CEU][hapmap]
rs6825635	0.82[CEU][hapmap]
rs6832294	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6839553	1.00[CEU][hapmap]
rs6845054	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6854192	0.82[CEU][hapmap]
rs72985392	0.87[EUR][1000 genomes]
rs7666494	0.94[CEU][hapmap]
rs7690646	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[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875801	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9998139	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv881602	chr4:172772005-172867912	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv596197	chr4:172797761-172868945	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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
7	nsv1029351	chr4:172809594-172893072	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	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
9	nsv870367	chr4:172834672-172867495	Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs179641	HMGB2	cis	cerebellum	SCAN
rs179641	GALNTL6	cis	cerebellum	SCAN
rs179641	GALNTL6	cis	parietal	SCAN

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

No data

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

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