Variant report

Variant	rs34650555
Chromosome Location	chr12:56465602-56465603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56464666..56467549-chr12:56498079..56499620,2	MCF-7	breast:
2	chr12:56435369..56438636-chr12:56464325..56466341,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170515	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000197728	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11171713	0.81[AMR][1000 genomes]
rs11171714	0.81[AMR][1000 genomes]
rs12099979	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12810011	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12815302	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12815387	0.92[EUR][1000 genomes]
rs12815488	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12817471	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12817765	0.81[AMR][1000 genomes]
rs12818756	1.00[EUR][1000 genomes]
rs12831468	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1614219	0.98[EUR][1000 genomes]
rs1689511	0.95[EUR][1000 genomes]
rs1701706	0.91[EUR][1000 genomes]
rs17118206	0.81[AMR][1000 genomes]
rs17118208	0.81[AMR][1000 genomes]
rs17118262	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131569	0.92[EUR][1000 genomes]
rs2229046	0.87[AMR][1000 genomes]
rs2456972	0.98[EUR][1000 genomes]
rs2658479	0.94[EUR][1000 genomes]
rs34071823	0.81[AMR][1000 genomes]
rs34228181	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34303864	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34406511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34485293	0.91[EUR][1000 genomes]
rs34507011	0.91[EUR][1000 genomes]
rs34602183	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34921584	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34962186	0.81[AMR][1000 genomes]
rs35485002	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs35662491	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35666826	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35961650	0.94[EUR][1000 genomes]
rs36035578	0.87[AMR][1000 genomes]
rs4759022	1.00[EUR][1000 genomes]
rs4759239	0.94[EUR][1000 genomes]
rs71447768	0.81[AMR][1000 genomes]
rs71459326	0.81[AMR][1000 genomes]
rs71459327	0.81[AMR][1000 genomes]
rs71459334	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459336	0.98[EUR][1000 genomes]
rs71459339	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459342	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7298818	0.94[EUR][1000 genomes]
rs7300772	0.98[EUR][1000 genomes]
rs772919	0.89[EUR][1000 genomes]
rs772922	0.91[EUR][1000 genomes]
rs772923	0.92[EUR][1000 genomes]
rs773115	0.94[EUR][1000 genomes]
rs7963590	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7977537	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34650555	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs34650555	SUOX	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
2	chr12:56454400-56467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:56456000-56465800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:56464800-56467200	Enhancers	Placenta	Placenta
5	chr12:56465000-56466200	Enhancers	NHDF-Ad	bronchial
6	chr12:56465000-56466400	Enhancers	NHEK	skin
7	chr12:56465000-56466600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:56465400-56466400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:56465400-56466600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:56465400-56467000	Enhancers	HepG2	liver
11	chr12:56465600-56466400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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