Variant report

Variant	rs11947923
Chromosome Location	chr4:53911337-53911338
allele	C/T
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:18)

rs_ID	r²[population]
rs1038355	0.92[CEU][hapmap];0.93[GIH][hapmap]
rs10517275	0.92[CEU][hapmap]
rs11934112	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs12506630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082398	0.82[GIH][hapmap]
rs2046306	0.88[CEU][hapmap]
rs2046307	0.92[CEU][hapmap];0.95[GIH][hapmap];0.93[MKK][hapmap]
rs3849654	0.82[GIH][hapmap]
rs4302515	0.84[CEU][hapmap]
rs4314341	0.91[CEU][hapmap]
rs4320191	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs6822251	0.92[CEU][hapmap]
rs6843335	0.92[CEU][hapmap];0.95[GIH][hapmap]
rs6846933	0.85[CEU][hapmap]
rs6847431	0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[MKK][hapmap]
rs7662427	0.92[CEU][hapmap]
rs7676982	0.92[CEU][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap]

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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11947923	HOPX	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53903000-53913400	Weak transcription	NHDF-Ad	bronchial
2	chr4:53904600-53921400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:53904800-53929800	Weak transcription	Primary T cells from cord blood	blood
4	chr4:53906200-53921400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:53906400-53921400	Weak transcription	NHLF	lung
6	chr4:53906800-53921400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:53907000-53921200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:53909000-53929400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:53909400-53911600	Enhancers	Fetal Brain Female	brain
10	chr4:53910400-53911400	Enhancers	Fetal Lung	lung

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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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