Variant report

Variant	rs6735555
Chromosome Location	chr2:231021064-231021065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10804362	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10804363	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12694843	0.81[EUR][1000 genomes]
rs1365773	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1365775	0.91[JPT][hapmap]
rs1427291	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1549567	0.91[JPT][hapmap]
rs1549571	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2396714	0.88[ASN][1000 genomes]
rs2894694	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4973276	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4973277	0.82[EUR][1000 genomes]
rs6721137	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7424288	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9807953	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv875943	chr2:230960946-231027162	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv520444	chr2:231014505-231021064	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv518470	chr2:231018169-231027162	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6735555	INPP5D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231018200-231022600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:231018200-231026000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:231019000-231022400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:231019200-231022800	Enhancers	Primary hematopoietic stem cells	blood
5	chr2:231019400-231024600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:231020200-231021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:231020400-231021600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:231020400-231022600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:231020600-231028400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:231021000-231022400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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