Variant report

Variant	rs1606265
Chromosome Location	chr3:145975039-145975040
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10460850	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11926040	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3762690	1.00[YRI][hapmap]
rs3920230	0.86[MKK][hapmap];1.00[YRI][hapmap]
rs4681298	1.00[YRI][hapmap]
rs4681300	1.00[YRI][hapmap]
rs6780480	1.00[YRI][hapmap]

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	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3333990	chr3:145950303-145982133	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv998388	chr3:145960954-146087749	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1606265	PLSCR4	cis	parietal	SCAN
rs1606265	PLSCR4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145974400-145975800	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr3:145974400-145976000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:145974600-145975200	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr3:145974600-145975200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:145974600-145975400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:145974600-145975800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:145974800-145975600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:145974800-145976000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:145975000-145975200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:145975000-145975400	Weak transcription	iPS-15b 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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