Variant report

Variant	rs17513809
Chromosome Location	chr6:139829917-139829918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs589235	0.84[ASN][1000 genomes]
rs592423	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs60562771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608736	0.84[ASN][1000 genomes]
rs628751	0.86[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs643381	0.84[ASN][1000 genomes]
rs72976928	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72976934	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72976941	0.94[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1026819	chr6:139813809-139834012	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17513809	MAP7	cis	cerebellum	SCAN
rs17513809	CACNA1G	trans	cerebellum	SCAN
rs17513809	CITED2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139828000-139831200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:139828800-139831800	Enhancers	HepG2	liver
3	chr6:139829200-139830600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:139829200-139832800	Enhancers	Fetal Heart	heart
5	chr6:139829600-139830600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:139829600-139831200	Weak transcription	K562	blood
7	chr6:139829600-139831600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:139829600-139835600	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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