Variant report

Variant	rs7562879
Chromosome Location	chr2:48983395-48983396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10176989	0.97[ASN][1000 genomes]
rs10180731	0.82[JPT][hapmap]
rs10194838	0.81[JPT][hapmap]
rs10209331	0.95[ASN][1000 genomes]
rs12615738	0.82[JPT][hapmap];0.83[YRI][hapmap]
rs13405728	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs13432488	0.88[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4075876	0.96[ASN][1000 genomes]
rs6732721	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7562215	0.83[ASW][hapmap]
rs7563126	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7567846	0.92[ASN][1000 genomes]
rs7582603	0.91[ASN][1000 genomes]
rs7595136	0.82[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7562879	FBXO11	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48982800-48983800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48983200-48983400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr2:48983200-48983400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr2:48983200-48983400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
5	chr2:48983200-48983400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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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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