Variant report

Variant	rs11180981
Chromosome Location	chr12:41925309-41925310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10459287	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785269	0.82[CEU][hapmap]
rs10880081	0.89[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880082	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10880086	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880087	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880088	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880089	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10880097	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180853	1.00[CHB][hapmap]
rs11180882	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11180936	0.84[CEU][hapmap]
rs11180943	0.88[CEU][hapmap]
rs11180961	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11180979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180980	1.00[JPT][hapmap]
rs11180984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180988	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180994	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12229610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372586	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12427081	1.00[CHB][hapmap]
rs1350431	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1379767	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1458153	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1458169	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1551594	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1589983	1.00[CHB][hapmap]
rs17579291	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1902908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054211	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608709	0.84[CEU][hapmap]
rs2733272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2733273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2733294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs285569	1.00[ASW][hapmap]
rs285583	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110189	0.84[CEU][hapmap]
rs3110389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768355	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs725527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73130674	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974539	1.00[JPT][hapmap]

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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11180981	PDZRN4	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41916000-41927400	Weak transcription	Aorta	Aorta
2	chr12:41924600-41925400	Enhancers	Colon Smooth Muscle	Colon
3	chr12:41924600-41925400	Enhancers	Fetal Muscle Trunk	muscle
4	chr12:41924600-41925400	Enhancers	Fetal Muscle Leg	muscle
5	chr12:41924600-41925600	Enhancers	Brain Substantia Nigra	brain
6	chr12:41924800-41925600	Enhancers	Brain Hippocampus Middle	brain
7	chr12:41925000-41925400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:41925000-41925600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:41925000-41925600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:41925200-41925400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:41925200-41925600	Enhancers	Brain Anterior Caudate	brain
12	chr12:41925200-41925600	Enhancers	Rectal Smooth Muscle	rectum
13	chr12:41925200-41925600	Enhancers	Stomach Smooth Muscle	stomach

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