Variant report

Variant	rs4593102
Chromosome Location	chr4:175356443-175356444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11936682	1.00[ASN][1000 genomes]
rs1922385	1.00[ASN][1000 genomes]
rs2244288	0.82[EUR][1000 genomes]
rs2555624	0.84[EUR][1000 genomes]
rs2555634	0.84[EUR][1000 genomes]
rs4499680	1.00[ASN][1000 genomes]
rs4554044	1.00[ASN][1000 genomes]
rs4624634	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs58587119	0.93[EUR][1000 genomes]
rs6553793	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66773185	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67034472	1.00[ASN][1000 genomes]
rs6821522	1.00[ASN][1000 genomes]
rs6833543	0.82[EUR][1000 genomes]
rs72704105	1.00[ASN][1000 genomes]
rs72704109	1.00[ASN][1000 genomes]
rs7660879	0.84[EUR][1000 genomes]
rs7673685	1.00[CHD][hapmap]
rs7677995	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4593102	FBXO8	cis	parietal	SCAN
rs4593102	HPGD	cis	multi-tissue	Pritchard
rs4593102	KIAA1712	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175350000-175358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:175352000-175357200	Weak transcription	A549	lung
3	chr4:175355400-175356800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:175355400-175357400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr4:175355600-175357400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:175356000-175357000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:175356000-175370800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:175356200-175356800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:175356200-175356800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr4:175356200-175358000	Weak transcription	Placenta	Placenta
11	chr4:175356400-175357200	Enhancers	Primary monocytes fromperipheralblood	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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