Variant report

Variant	rs71459342
Chromosome Location	chr12:56470778-56470779
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56467571..56470016-chr12:56470633..56472674,2	K562	blood:
2	chr12:56434525..56442579-chr12:56469196..56475242,12	K562	blood:

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12099979	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12810011	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12815302	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12815387	0.81[EUR][1000 genomes]
rs12815488	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12817471	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12818756	0.89[EUR][1000 genomes]
rs12831468	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1614219	0.87[EUR][1000 genomes]
rs1689511	0.84[EUR][1000 genomes]
rs17118262	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2131569	0.81[EUR][1000 genomes]
rs2229046	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2456972	0.87[EUR][1000 genomes]
rs2658479	0.83[EUR][1000 genomes]
rs34228181	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34303864	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34406511	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34485293	0.80[EUR][1000 genomes]
rs34602183	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34650555	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34921584	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35485002	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35662491	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35666826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35961650	0.83[EUR][1000 genomes]
rs36035578	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4759022	0.89[EUR][1000 genomes]
rs4759239	0.83[EUR][1000 genomes]
rs71459334	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs71459336	0.87[EUR][1000 genomes]
rs71459339	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7298818	0.87[EUR][1000 genomes]
rs7300772	0.87[EUR][1000 genomes]
rs772923	0.81[EUR][1000 genomes]
rs773115	0.83[EUR][1000 genomes]
rs7963590	0.81[EUR][1000 genomes]
rs7977537	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][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	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	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71459342	SUOX	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
2	chr12:56466200-56472400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:56466400-56471800	Weak transcription	Hela-S3	cervix
4	chr12:56466400-56472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:56466600-56472600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:56466600-56472800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:56468000-56472800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:56468200-56472600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:56468600-56472600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:56468800-56471400	Weak transcription	HepG2	liver
11	chr12:56470400-56472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:56470400-56472600	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links