Variant report

Variant	rs12416046
Chromosome Location	chr10:89861218-89861219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10749564	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11202654	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932532	0.83[JPT][hapmap]
rs1981150	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4147056	0.83[JPT][hapmap];0.94[AMR][1000 genomes]
rs4933467	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7070980	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7079754	0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12416046	PANK1	cis	cerebellum	SCAN
rs12416046	SNCG	cis	cerebellum	SCAN
rs12416046	FAS	cis	parietal	SCAN
rs12416046	LDB3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89856000-89864800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:89858600-89863200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr10:89859200-89861400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr10:89860000-89861600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:89860400-89861400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr10:89860800-89861600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr10:89860800-89864200	Enhancers	GM12878-XiMat	blood
8	chr10:89861000-89861600	Enhancers	Primary B cells from cord blood	blood
9	chr10:89861000-89863800	Weak transcription	Primary B cells from peripheral blood	blood

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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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