Variant report

Variant	rs9821525
Chromosome Location	chr3:60898109-60898110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11130793	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11130794	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130795	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs11130800	0.91[ASW][hapmap];1.00[YRI][hapmap]
rs11708288	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12493259	1.00[YRI][hapmap]
rs1562519	0.85[CHB][hapmap]
rs1562524	0.86[JPT][hapmap]
rs1562525	0.86[JPT][hapmap]
rs3952441	1.00[YRI][hapmap]
rs4974249	0.91[ASW][hapmap];1.00[YRI][hapmap]
rs6804478	0.93[CHD][hapmap]
rs9851616	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534038	chr3:60781917-60993082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757872	chr3:60781943-61019003	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9821525	SLMAP	cis	parietal	SCAN
rs9821525	DNAH12	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60885800-60902200	Weak transcription	Ovary	ovary
2	chr3:60897600-60899200	Enhancers	HMEC	breast
3	chr3:60897600-60899600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:60897600-60899600	Enhancers	NHEK	skin
5	chr3:60897800-60899600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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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

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