Variant report

Variant	rs1475820
Chromosome Location	chr9:73059817-73059818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10780934	0.84[EUR][1000 genomes]
rs11142419	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11142421	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13302860	0.82[ASW][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs17455513	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17455773	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17534370	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41530345	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73462451	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73462466	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73462472	0.84[EUR][1000 genomes]
rs73462475	0.84[EUR][1000 genomes]
rs73462482	0.82[EUR][1000 genomes]
rs7853214	0.84[EUR][1000 genomes]
rs915489	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs915490	1.00[AMR][1000 genomes];0.99[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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv428219	chr9:73006269-73192535	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1475820	MAMDC2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73053600-73071000	Weak transcription	Right Atrium	heart
2	chr9:73054000-73065000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:73054400-73066600	Weak transcription	Psoas Muscle	Psoas
4	chr9:73057800-73061600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:73059600-73060200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr9:73059600-73060400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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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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