Variant report

Variant	rs338021
Chromosome Location	chr4:173399986-173399987
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10004745	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs10019934	0.96[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10024431	0.84[CEU][hapmap]
rs10029297	0.81[CHB][hapmap]
rs10434403	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs11132944	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs11132945	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11132946	0.99[ASN][1000 genomes]
rs13116631	0.84[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs13435174	1.00[CEU][hapmap]
rs1995068	0.96[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2047342	0.96[CEU][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap]
rs2332535	0.96[CEU][hapmap]
rs28726202	0.86[EUR][1000 genomes]
rs2877713	0.96[CEU][hapmap]
rs3104246	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs336005	0.81[CHB][hapmap]
rs336006	0.81[CHB][hapmap]
rs336014	0.81[CHB][hapmap]
rs336016	0.81[CHB][hapmap]
rs336017	0.81[CHB][hapmap]
rs336019	0.85[CHB][hapmap]
rs336021	0.81[CHB][hapmap]
rs337051	0.84[CHB][hapmap]
rs337053	0.88[CHB][hapmap]
rs337984	0.81[CHB][hapmap]
rs337986	0.87[ASN][1000 genomes]
rs337988	0.81[CHB][hapmap];0.96[ASN][1000 genomes]
rs337989	0.99[ASN][1000 genomes]
rs337990	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs337991	0.80[CHB][hapmap];0.99[ASN][1000 genomes]
rs337992	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs337993	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs338007	0.87[ASN][1000 genomes]
rs338027	0.99[ASN][1000 genomes]
rs338028	0.99[ASN][1000 genomes]
rs338029	0.96[ASN][1000 genomes]
rs338030	0.97[ASN][1000 genomes]
rs488103	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs6815640	0.81[CHB][hapmap]
rs6816068	0.96[CEU][hapmap]
rs6821570	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs744775	0.82[CHB][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	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1031327	chr4:173306405-173465248	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv508333	chr4:173369686-173447675	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs338021	GALNTL6	cis	cerebellum	SCAN
rs338021	WDR17	cis	cerebellum	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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