Variant report

Variant	rs7838646
Chromosome Location	chr8:60525796-60525797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10107875	0.97[EUR][1000 genomes]
rs12547681	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12549965	0.97[EUR][1000 genomes]
rs28679689	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4342576	0.89[EUR][1000 genomes]
rs4737547	0.89[EUR][1000 genomes]
rs6471795	0.83[EUR][1000 genomes]
rs6982265	0.94[EUR][1000 genomes]
rs6983204	0.89[EUR][1000 genomes]
rs6986251	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6990717	0.97[EUR][1000 genomes]
rs7008068	0.95[EUR][1000 genomes]
rs7014422	0.89[EUR][1000 genomes]
rs7828085	0.88[EUR][1000 genomes]
rs7828435	0.94[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	nsv1029441	chr8:60099776-60539141	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539629	chr8:60099776-60539141	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1030564	chr8:60445016-60752655	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv539630	chr8:60445016-60752655	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7838646	LOC643763	cis	parietal	SCAN
rs7838646	CDCA2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:60525000-60526200	Enhancers	Colon Smooth Muscle	Colon
2	chr8:60525000-60526400	Enhancers	Rectal Smooth Muscle	rectum
3	chr8:60525600-60526200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr8:60525600-60526400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr8:60525600-60529000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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