Variant report

Variant	rs11958129
Chromosome Location	chr5:108343438-108343439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10043207	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10062069	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10447249	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11240990	0.80[ASN][1000 genomes]
rs11948270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11948684	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11949648	0.93[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap]
rs11951285	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[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]
rs11951595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11954988	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11955924	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]
rs11956572	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11956900	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11958918	0.81[LWK][hapmap]
rs11960268	0.86[EUR][1000 genomes]
rs11960336	0.86[EUR][1000 genomes]
rs11960400	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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12152788	1.00[ASN][1000 genomes]
rs12153527	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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12153646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12186663	0.95[ASN][1000 genomes]
rs12188107	1.00[ASN][1000 genomes]
rs12188521	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1366081	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17534347	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17534396	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1896582	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2416196	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2416197	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3797823	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs3797825	0.82[CEU][hapmap]
rs3797827	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797830	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797832	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3797833	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3797834	1.00[JPT][hapmap]
rs3797837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3797847	1.00[JPT][hapmap]
rs3822684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822685	1.00[JPT][hapmap]
rs3851457	0.81[LWK][hapmap]
rs4404726	0.89[EUR][1000 genomes]
rs4957795	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs55899933	0.91[EUR][1000 genomes]
rs56083128	0.95[ASN][1000 genomes]
rs56382548	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57221554	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57814250	0.86[EUR][1000 genomes]
rs58255942	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58499805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58729959	0.86[EUR][1000 genomes]
rs59409290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60584949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60834821	0.91[EUR][1000 genomes]
rs61304250	0.95[ASN][1000 genomes]
rs66623856	0.82[EUR][1000 genomes]
rs6865572	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6867147	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6869929	0.95[ASN][1000 genomes]
rs6872299	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6882698	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6884133	1.00[JPT][hapmap]
rs6886017	0.95[ASN][1000 genomes]
rs6889213	0.95[ASN][1000 genomes]
rs6893501	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs72789336	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72789338	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72789339	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790513	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790518	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790522	1.00[ASN][1000 genomes]
rs72790537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790569	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790570	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790571	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73778341	0.95[ASN][1000 genomes]
rs73778362	0.95[ASN][1000 genomes]
rs73778371	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73778393	0.96[ASN][1000 genomes]
rs73778394	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73779105	0.95[ASN][1000 genomes]
rs73779109	0.95[ASN][1000 genomes]
rs73779112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73779120	0.95[ASN][1000 genomes]
rs73780404	1.00[ASN][1000 genomes]
rs73780405	1.00[ASN][1000 genomes]
rs73780406	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73781919	0.95[ASN][1000 genomes]
rs73781924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7702557	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7709840	0.84[JPT][hapmap]
rs7714599	1.00[JPT][hapmap]
rs7718925	1.00[JPT][hapmap]
rs7719229	1.00[ASN][1000 genomes]
rs7723580	1.00[ASN][1000 genomes]
rs7723942	0.81[EUR][1000 genomes]
rs7725708	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7726922	0.88[EUR][1000 genomes]
rs7729380	1.00[JPT][hapmap]
rs7732335	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7732510	0.81[EUR][1000 genomes]
rs7733971	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7734092	0.82[GIH][hapmap]
rs7734110	0.82[GIH][hapmap]
rs7734437	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs919771	0.85[LWK][hapmap]
rs9688204	1.00[ASN][1000 genomes]
rs9688214	1.00[ASN][1000 genomes]
rs9885203	0.85[CHB][hapmap];0.86[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	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv4952	chr5:108324146-108369353	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11958129	MCC	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108301600-108361200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:108329600-108346200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:108329600-108359600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:108330200-108351800	Weak transcription	Fetal Lung	lung
5	chr5:108332600-108359400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:108332800-108359800	Weak transcription	Adipose Nuclei	Adipose
7	chr5:108333400-108351600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:108334200-108344200	Weak transcription	Fetal Stomach	stomach
9	chr5:108341000-108360000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:108341200-108359800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:108341800-108359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:108342200-108359800	Weak transcription	NHEK	skin

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