Variant report

Variant	rs479336
Chromosome Location	chr1:172199573-172199574
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10911387	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11808940	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12049422	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs12402454	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs12410416	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs12411264	0.80[CHD][hapmap];0.80[JPT][hapmap]
rs2586389	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2586392	1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2586394	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2586403	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2586404	0.93[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs2586408	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs2586410	0.93[CEU][hapmap]
rs2586411	0.93[CEU][hapmap]
rs2586412	0.93[CEU][hapmap]
rs2586413	0.93[CEU][hapmap]
rs2757493	0.93[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2757495	0.93[CEU][hapmap]
rs2757496	0.81[AMR][1000 genomes]
rs41516352	0.80[JPT][hapmap]
rs477289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6701929	1.00[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs678962	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs7550558	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][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	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv465650	chr1:172175115-172247127	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv548192	chr1:172175115-172247127	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv872546	chr1:172186321-172219995	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22504420	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs479336	CREG1	cis	cerebellum	SCAN
rs479336	F5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172194200-172199800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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