Variant report

Variant	rs530752
Chromosome Location	chr11:62671014-62671015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000168539	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000162236	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000256690	Chromatin interaction
ENSG00000255717	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11568621	1.00[JPT][hapmap]
rs11568628	1.00[JPT][hapmap]
rs11568629	1.00[JPT][hapmap]
rs11823728	0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2067478	0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
4	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
5	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	263 gene(s)	inside rSNPs	diseases
6	esv34011	chr11:62652779-62993702	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs530752	RNU25	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62664000-62673000	Weak transcription	Brain Anterior Caudate	brain
2	chr11:62665000-62671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr11:62666400-62673400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr11:62666800-62672400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:62667000-62672800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:62669400-62671200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:62669600-62671200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:62669800-62671200	Enhancers	GM12878-XiMat	blood
9	chr11:62670000-62671200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:62670400-62671200	Enhancers	HMEC	breast
11	chr11:62670400-62671200	Enhancers	NHLF	lung
12	chr11:62670600-62671200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:62670800-62671200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr11:62670800-62673000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:62671000-62671200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:62671000-62671200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:62671000-62671200	Enhancers	Right Atrium	heart

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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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