Variant report

Variant	rs726169
Chromosome Location	chr1:239794277-239794278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10925943	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12057204	0.90[ASN][1000 genomes]
rs12063338	0.90[ASN][1000 genomes]
rs12090420	0.90[ASN][1000 genomes]
rs12090480	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12094134	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12097526	0.85[ASN][1000 genomes]
rs16832153	0.89[ASN][1000 genomes]
rs4465191	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6429148	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6691263	0.90[ASN][1000 genomes]
rs6692904	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6701925	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv873352	chr1:239755406-239798412	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv468628	chr1:239774670-239812103	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv468639	chr1:239774670-239812103	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv549438	chr1:239774670-239812103	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv549439	chr1:239785165-239800028	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs726169	ZP4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239793200-239796600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:239793200-239797200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:239793400-239796600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:239793600-239797000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:239793800-239794400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:239794000-239794400	Enhancers	Pancreas	Pancrea
7	chr1:239794000-239795400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:239794200-239794600	Weak transcription	Primary T cells from cord blood	blood
9	chr1:239794200-239794800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:239794200-239796600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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