Variant report

Variant	rs12539820
Chromosome Location	chr7:108323386-108323387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12534347	0.88[EUR][1000 genomes]
rs12536143	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12705492	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13243000	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1544347	0.85[EUR][1000 genomes]
rs17156107	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17350594	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193454	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964202	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35307180	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35826348	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36012065	0.85[EUR][1000 genomes]
rs40957	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6948908	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6949511	0.82[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	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1023651	chr7:108303048-108385180	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12539820	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108323200-108323800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:108323200-108323800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:108323200-108324000	Enhancers	Adipose Nuclei	Adipose
4	chr7:108323200-108324200	Enhancers	Adipose Derived Mesenchymal Stem Cell 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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