Variant report

Variant	rs16832279
Chromosome Location	chr3:161120483-161120484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
2	chr10:91899658..91901656-chr3:161118536..161120894,2	MCF-7	breast:
3	chr3:161119895..161121991-chr3:161159318..161161280,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11710086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11710916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711695	0.81[GIH][hapmap]
rs11713185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1349352	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450522	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs16832246	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1811483	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1839491	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054710	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs2061804	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2404341	0.90[CHB][hapmap]
rs2404342	0.85[CHB][hapmap]
rs34727114	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs404725	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs456882	0.83[ASN][1000 genomes]
rs458175	0.83[ASN][1000 genomes]
rs460950	0.83[ASN][1000 genomes]
rs463630	0.83[ASN][1000 genomes]
rs463890	0.83[ASN][1000 genomes]
rs466971	0.82[ASN][1000 genomes]
rs467458	0.83[ASN][1000 genomes]
rs6441374	0.81[CHD][hapmap]
rs67077657	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73021449	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627320	0.90[JPT][hapmap]
rs9816665	0.90[JPT][hapmap]
rs9836881	0.90[JPT][hapmap]
rs9836887	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
5	nsv524747	chr3:161120483-161123526	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16832279	PPM1L	cis	cerebellum	SCAN
rs16832279	SPTSSB	cis	Thyroid	GTEx
rs16832279	NMD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161113600-161127600	Weak transcription	NHEK	skin
2	chr3:161119000-161120800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:161119000-161124400	Weak transcription	Liver	Liver
4	chr3:161119800-161120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:161119800-161120800	Weak transcription	NHDF-Ad	bronchial
6	chr3:161120400-161123000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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