Variant report

Variant	rs11980087
Chromosome Location	chr7:38725804-38725805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11772698	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12701651	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1864886	0.81[GIH][hapmap]
rs7783695	0.81[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7810938	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9692361	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11980087	CDK2AP1	trans	parietal	SCAN
rs11980087	TARP	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38696000-38726000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:38722200-38733800	Weak transcription	Right Atrium	heart
3	chr7:38725600-38726400	Enhancers	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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