Variant report

Variant	rs2959024
Chromosome Location	chr8:105479771-105479772
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1355691	0.80[TSI][hapmap]
rs2959025	0.82[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3018436	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3018439	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3110525	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[ASN][1000 genomes]
rs3134531	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3134532	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7461146	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	esv3328158	chr8:105477801-105480349	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2959024	LRP12	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105479600-105479800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
2	chr8:105479600-105479800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr8:105479600-105479800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr8:105479600-105479800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr8:105479600-105479800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr8:105479600-105479800	Bivalent Enhancer	Stomach Mucosa	stomach
7	chr8:105479600-105480600	Enhancers	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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