Variant report

Variant	rs12487861
Chromosome Location	chr3:160535721-160535722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160535684..160538516-chr3:160543407..160545193,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513553	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12494732	0.85[JPT][hapmap]
rs13080397	0.86[CEU][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs1378654	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1378657	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1378658	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1455869	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap]
rs1598495	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs16831457	0.82[YRI][hapmap]
rs1829716	0.89[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs1839017	0.85[JPT][hapmap]
rs1851378	0.89[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs1902282	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1915929	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049214	0.89[ASN][1000 genomes]
rs2049215	0.89[ASN][1000 genomes]
rs4256178	0.86[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs59542611	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794047	0.89[ASN][1000 genomes]
rs718757	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs722871	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7618832	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs7630250	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633401	0.86[YRI][hapmap]
rs7648363	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs779058	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs972909	0.89[ASN][1000 genomes]
rs9815499	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs9824439	0.91[EUR][1000 genomes]
rs9833075	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9866566	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868489	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9869116	0.85[JPT][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv432495	chr3:160534298-160548298	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12487861	PPM1L	cis	cerebellum	SCAN
rs12487861	IFT80	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160528200-160537600	Weak transcription	Hela-S3	cervix
2	chr3:160530600-160536000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:160530600-160537800	Weak transcription	Gastric	stomach
4	chr3:160530800-160540800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:160530800-160543200	Weak transcription	Psoas Muscle	Psoas
6	chr3:160534200-160536600	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links