Variant report

Variant	rs9408863
Chromosome Location	chr9:118145764-118145765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10124685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817756	0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs10817758	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982719	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982722	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982724	0.81[GIH][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982725	0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10982726	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11791418	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs12336386	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750505	0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs7018671	0.81[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs7040283	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7040762	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9408864	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9408865	0.83[ASN][1000 genomes]
rs9409148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409149	0.81[GIH][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9409150	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs981911	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2761552	chr9:118113846-118157488	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9408863	C9orf29	cis	parietal	SCAN
rs9408863	ZNF618	cis	parietal	SCAN
rs9408863	DNAJC25	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118144800-118146000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:118144800-118146000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:118145400-118147800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:118145600-118149600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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