Variant report

Variant	rs11168599
Chromosome Location	chr12:48879951-48879952
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48877425..48880282-chr12:48884726..48886278,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10875827	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875829	0.89[EUR][1000 genomes]
rs10875833	0.83[EUR][1000 genomes]
rs11168577	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168586	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168618	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168619	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168637	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs11458	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371700	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425460	0.83[TSI][hapmap]
rs12815544	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2114322	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2731091	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2731094	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2731095	0.85[ASN][1000 genomes]
rs2731097	0.84[ASN][1000 genomes]
rs2731102	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2731107	0.85[ASN][1000 genomes]
rs35338015	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4359253	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57444623	0.99[ASN][1000 genomes]
rs6580671	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7301176	0.87[CHD][hapmap]
rs7302209	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312017	0.94[JPT][hapmap]
rs7955785	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7972785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974213	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976324	0.82[EUR][1000 genomes]
rs7980421	0.83[EUR][1000 genomes]
rs9268	0.92[CHB][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv975415	chr12:48873981-48881500	Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11168599	OR10AD1	cis	cerebellum	SCAN
rs11168599	RPAP3	cis	cerebellum	SCAN
rs11168599	CCNT1	cis	cerebellum	SCAN
rs11168599	IGJ	trans	parietal	SCAN
rs11168599	ADAMTS20	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48879800-48880400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:48879800-48880400	Enhancers	NHEK	skin
3	chr12:48879800-48881200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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