Variant report

Variant	rs9878975
Chromosome Location	chr3:43168222-43168223
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11707627	0.81[EUR][1000 genomes]
rs11707725	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11715255	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11716441	0.83[ASN][1000 genomes]
rs11719553	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11719573	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17075162	0.82[EUR][1000 genomes]
rs1851577	0.82[EUR][1000 genomes]
rs28376397	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57549659	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60879744	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs627582	0.81[EUR][1000 genomes]
rs737351	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7619872	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9878975	SLC6A20	cis	parietal	SCAN
rs9878975	CCR8	cis	cerebellum	SCAN
rs9878975	HIGD1A	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43167800-43170400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:43168200-43169600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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