Variant report

Variant	rs6433953
Chromosome Location	chr2:182911702-182911703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:182911673-182912987	SK-N-SH	brain:	n/a	chr2:182912089-182912097 chr2:182912374-182912388 chr2:182912552-182912566 chr2:182912515-182912529 chr2:182912662-182912672
2	POLR2A	chr2:182911570-182912005	SK-N-MC	brain:	n/a	n/a
3	PBX3	chr2:182911566-182912925	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP113	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1196155	0.94[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1196157	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs1196160	0.94[CEU][hapmap];0.86[CHD][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1196167	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs1196179	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1196183	0.83[EUR][1000 genomes]
rs1196185	0.89[CEU][hapmap];0.81[CHD][hapmap];0.87[TSI][hapmap]
rs12693291	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13017711	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1400010	0.83[EUR][1000 genomes]
rs16822401	0.94[CEU][hapmap]
rs16822409	0.94[CEU][hapmap]
rs1913896	0.88[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2701664	0.94[CEU][hapmap];0.86[CHD][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2701665	0.94[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6732434	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6747855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7560061	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7589699	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6433953	PPP1R1C	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182903200-182928400	Weak transcription	Left Ventricle	heart
2	chr2:182904000-182912000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:182907400-182912200	Weak transcription	Osteobl	bone
4	chr2:182907600-182911800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:182907600-182915600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:182908000-182912000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links