Variant report

Variant	rs11779980
Chromosome Location	chr8:124922736-124922737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:124915045..124918415-chr8:124921775..124925187,3	MCF-7	breast:
2	chr8:124843791..124846042-chr8:124921858..124924618,2	MCF-7	breast:
3	chr8:124918718..124920943-chr8:124922678..124925068,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10089499	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10089757	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs10103366	0.91[CEU][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap]
rs10110548	0.91[CEU][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10956153	0.95[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10956154	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956155	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956156	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782845	0.91[CEU][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11787464	0.95[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12541526	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12544278	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12548182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548510	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550262	0.95[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1816368	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs28425543	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703921	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61030560	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6998986	0.91[CEU][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap]
rs7823205	0.86[CEU][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap]
rs7844410	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656949	0.91[CEU][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv1033617	chr8:124895516-125012783	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1035035	chr8:124895516-125020472	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv612141	chr8:124895809-125006490	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv612142	chr8:124896389-125006490	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11779980	MRPL13	cis	parietal	SCAN
rs11779980	WDR67	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124919000-124923600	Weak transcription	Adipose Nuclei	Adipose
2	chr8:124919600-124923200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:124920200-124923000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr8:124920800-124923600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr8:124921400-124922800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links