Variant report

Variant	rs2424559
Chromosome Location	chr20:23430519-23430520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1016628	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2064587	0.80[GIH][hapmap]
rs2180139	0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2243448	0.85[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2253834	0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2281431	0.80[EUR][1000 genomes]
rs2295239	0.80[EUR][1000 genomes]
rs2424542	0.80[EUR][1000 genomes]
rs2424555	0.82[EUR][1000 genomes]
rs2424558	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3746736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142246	0.80[EUR][1000 genomes]
rs6048760	0.85[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs6048779	0.80[EUR][1000 genomes]
rs6048781	0.80[EUR][1000 genomes]
rs6048784	0.80[EUR][1000 genomes]
rs6083127	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6137933	0.80[EUR][1000 genomes]
rs999068	0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv979404	chr20:23429655-23455778	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2424559	NAPB	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23417200-23434800	Weak transcription	Gastric	stomach
2	chr20:23417800-23441000	Weak transcription	Right Atrium	heart
3	chr20:23423000-23432200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:23423800-23432200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:23427800-23431600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr20:23429600-23431200	Enhancers	Fetal Thymus	thymus
7	chr20:23429800-23430600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr20:23429800-23430600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr20:23429800-23430600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:23429800-23430600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:23430000-23430600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr20:23430000-23430600	Enhancers	Dnd41	blood
13	chr20:23430000-23430800	Enhancers	Primary T cells from cord blood	blood
14	chr20:23430400-23436200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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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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