Variant report

Variant	rs11458
Chromosome Location	chr12:48888594-48888595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48887453..48890090-chr12:48892571..48894412,2	MCF-7	breast:
2	chr12:48887538..48890353-chr12:48917589..48920002,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR8S1-2	chr12:48888581-48888762	NONHSAT028007

Variant related genes	Relation type
ENSG00000197376	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10875827	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875829	0.93[EUR][1000 genomes]
rs10875833	0.86[EUR][1000 genomes]
rs11168577	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168586	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168599	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]
rs11168618	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168619	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168637	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs12371700	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[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];0.87[EUR][1000 genomes]
rs2114322	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[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	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4359253	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57444623	0.99[ASN][1000 genomes]
rs6580671	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7301176	0.87[CHD][hapmap]
rs7302209	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312017	0.94[JPT][hapmap]
rs7955785	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7972785	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974213	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][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]
rs7976324	0.85[EUR][1000 genomes]
rs7980421	0.87[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	nsv975416	chr12:48882416-48893049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11458	RPAP3	cis	cerebellum	SCAN
rs11458	CCNT1	cis	cerebellum	SCAN
rs11458	ADAMTS20	cis	cerebellum	SCAN
rs11458	OR10AD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48887000-48891800	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:48887600-48890000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:48888000-48888600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:48888400-48888600	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links