Variant report

Variant	rs59122847
Chromosome Location	chr6:81065102-81065103
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1320614	0.80[AMR][1000 genomes]
rs1320615	0.80[AMR][1000 genomes]
rs4134487	0.80[AMR][1000 genomes]
rs7745921	0.80[AMR][1000 genomes]
rs7766087	0.80[AMR][1000 genomes]
rs7766633	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv463907	chr6:81047559-81075912	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv604053	chr6:81047559-81075912	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59122847	BCKDHB	cis	Thyroid	GTEx
rs59122847	BCKDHB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81029400-81079600	Weak transcription	HSMM	muscle
2	chr6:81033800-81070200	Weak transcription	Left Ventricle	heart
3	chr6:81048200-81066800	Weak transcription	Pancreas	Pancrea
4	chr6:81050400-81071200	Weak transcription	Primary T cells from cord blood	blood
5	chr6:81053600-81073800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:81057200-81067200	Weak transcription	Fetal Lung	lung
7	chr6:81058400-81067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:81058400-81071400	Weak transcription	Aorta	Aorta
9	chr6:81058400-81075800	Weak transcription	Psoas Muscle	Psoas
10	chr6:81059200-81069000	Weak transcription	Fetal Stomach	stomach
11	chr6:81060600-81069000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:81062600-81067000	Weak transcription	NHDF-Ad	bronchial
13	chr6:81063000-81070400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:81063800-81066800	Weak transcription	Adipose Nuclei	Adipose
15	chr6:81063800-81067000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:81063800-81068800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:81064000-81069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:81064600-81068800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:81065000-81066800	Weak transcription	Liver	Liver

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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