Variant report

Variant	rs12439488
Chromosome Location	chr15:41894575-41894576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1106934	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs11858843	0.81[CHB][hapmap]
rs1197659	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs1197773	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs12439771	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs12591253	0.83[AMR][1000 genomes]
rs12591285	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs12595271	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12901742	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs16971915	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes]
rs1819454	0.81[ASN][1000 genomes]
rs1918312	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs1918313	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs2077361	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs2577949	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs28896245	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34405276	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4072386	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4923906	1.00[CEU][hapmap]
rs4923907	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs4924573	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7168386	0.84[AMR][1000 genomes]
rs7173431	0.81[AMR][1000 genomes]
rs7173779	0.92[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs7177495	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs8024907	0.84[AMR][1000 genomes]
rs8026106	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9788715	0.83[AMR][1000 genomes]
rs9788733	0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12439488	ZFYVE19	cis	parietal	SCAN
rs12439488	INO80	cis	cerebellum	SCAN
rs12439488	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs12439488	NUSAP1	cis	cerebellum	SCAN
rs12439488	VPS18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41881200-41895800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:41889600-41895000	Weak transcription	K562	blood
3	chr15:41891200-41896000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:41891400-41896000	Weak transcription	Ovary	ovary
5	chr15:41893000-41896000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:41893200-41895800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:41893200-41895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:41893200-41896200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:41893400-41895800	Weak transcription	Fetal Heart	heart
10	chr15:41893400-41896400	Weak transcription	Fetal Kidney	kidney

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