Variant report

Variant	rs13003589
Chromosome Location	chr2:182887596-182887597
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:182602919..182608806-chr2:182883835..182887841,7	MCF-7	breast:
2	chr2:182775265..182779288-chr2:182885219..182887763,3	MCF-7	breast:
3	chr2:182880540..182889219-chr2:182930483..182937514,17	MCF-7	breast:
4	chr2:182878350..182883617-chr2:182884641..182888824,4	MCF-7	breast:
5	chr2:182754599..182765670-chr2:182881701..182887661,28	MCF-7	breast:
6	chr2:182884188..182888119-chr2:182990048..182995139,6	MCF-7	breast:
7	chr2:182880362..182889935-chr2:182937119..182944893,30	MCF-7	breast:
8	chr2:182885316..182887646-chr2:182929633..182931322,2	MCF-7	breast:
9	chr2:182885247..182888264-chr2:182945298..182948359,3	MCF-7	breast:
10	chr2:182880158..182888359-chr2:182937576..182947086,29	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000221023	Chromatin interaction
ENSG00000138434	Chromatin interaction
ENSG00000260742	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1196155	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1196157	0.90[CEU][hapmap]
rs1196160	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1196167	0.89[CEU][hapmap]
rs1196179	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1196183	0.85[EUR][1000 genomes]
rs1196185	0.89[CEU][hapmap]
rs12693291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12693292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13017711	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1400010	0.82[EUR][1000 genomes]
rs16822401	0.94[CEU][hapmap]
rs16822409	0.90[CEU][hapmap]
rs1913896	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2701664	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2701665	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6433953	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]
rs6732434	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6747855	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560061	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7589699	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	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
3	nsv834479	chr2:182738483-182905444	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13003589	PPP1R1C	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182843400-182904000	Weak transcription	Thymus	Thymus
2	chr2:182884800-182888400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:182886800-182888200	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links