Variant report

Variant	rs11954988
Chromosome Location	chr5:108343182-108343183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10447249	0.83[AFR][1000 genomes]
rs11948684	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs11948881	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11949066	0.86[EUR][1000 genomes]
rs11949367	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11949510	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11949619	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11949648	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11949706	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11951285	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11951595	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11951971	0.98[EUR][1000 genomes]
rs11951974	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952227	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11952572	0.86[EUR][1000 genomes]
rs11953136	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11953486	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11954716	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11955886	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11955924	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11956908	0.93[EUR][1000 genomes]
rs11957358	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11958129	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11958918	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11959492	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11959577	0.95[EUR][1000 genomes]
rs11959681	1.00[CEU][hapmap]
rs11960400	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12153527	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12153646	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12188521	0.84[AFR][1000 genomes]
rs17534347	0.89[AFR][1000 genomes]
rs17534354	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17534396	0.82[YRI][hapmap]
rs34412145	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34679271	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3797827	0.89[AFR][1000 genomes]
rs3797830	0.89[AFR][1000 genomes]
rs3822684	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3851457	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3851458	0.93[EUR][1000 genomes]
rs4957795	1.00[YRI][hapmap]
rs56381733	0.82[EUR][1000 genomes]
rs56382548	0.85[AFR][1000 genomes]
rs57404758	0.87[EUR][1000 genomes]
rs57622369	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58255942	0.91[AFR][1000 genomes]
rs59055229	0.82[EUR][1000 genomes]
rs59216020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59409290	0.89[AFR][1000 genomes]
rs60584949	0.89[AFR][1000 genomes]
rs60946864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67338203	0.82[EUR][1000 genomes]
rs72787096	0.88[EUR][1000 genomes]
rs72787098	0.88[EUR][1000 genomes]
rs72787099	0.87[EUR][1000 genomes]
rs72787100	0.88[EUR][1000 genomes]
rs72787101	0.88[EUR][1000 genomes]
rs72787102	0.88[EUR][1000 genomes]
rs72789304	0.88[EUR][1000 genomes]
rs72789305	0.87[EUR][1000 genomes]
rs72789306	0.88[EUR][1000 genomes]
rs72789307	0.88[EUR][1000 genomes]
rs72789308	0.88[EUR][1000 genomes]
rs72789309	0.88[EUR][1000 genomes]
rs72789312	0.91[EUR][1000 genomes]
rs72789313	0.91[EUR][1000 genomes]
rs72789315	0.92[EUR][1000 genomes]
rs72789316	0.93[EUR][1000 genomes]
rs72789319	0.93[EUR][1000 genomes]
rs72789320	0.92[EUR][1000 genomes]
rs72789326	0.93[EUR][1000 genomes]
rs72789332	0.93[EUR][1000 genomes]
rs72789333	0.92[EUR][1000 genomes]
rs72789335	0.93[EUR][1000 genomes]
rs72789341	0.93[EUR][1000 genomes]
rs72789345	0.93[EUR][1000 genomes]
rs72789347	0.93[EUR][1000 genomes]
rs72789348	0.93[EUR][1000 genomes]
rs72789350	0.93[EUR][1000 genomes]
rs72789352	0.92[EUR][1000 genomes]
rs72790510	0.93[EUR][1000 genomes]
rs72790512	0.93[EUR][1000 genomes]
rs72790514	0.93[EUR][1000 genomes]
rs72790515	0.93[EUR][1000 genomes]
rs72790520	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72790521	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72790524	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790528	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790537	0.89[AFR][1000 genomes]
rs72790538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790542	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790543	0.89[AFR][1000 genomes]
rs72790544	0.89[AFR][1000 genomes]
rs72790545	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790546	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790548	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790552	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790554	0.89[AFR][1000 genomes]
rs72790558	0.89[AFR][1000 genomes]
rs72790559	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72790562	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790564	0.89[AFR][1000 genomes]
rs72790565	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790567	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790568	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790570	0.81[AFR][1000 genomes]
rs72790571	0.89[AFR][1000 genomes]
rs72790572	0.89[AFR][1000 genomes]
rs72790574	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790577	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790579	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72790585	0.82[EUR][1000 genomes]
rs72793918	0.84[EUR][1000 genomes]
rs72793920	0.84[EUR][1000 genomes]
rs72793922	0.84[EUR][1000 genomes]
rs72793923	0.84[EUR][1000 genomes]
rs72793926	0.88[EUR][1000 genomes]
rs72793927	0.88[EUR][1000 genomes]
rs72793933	0.88[EUR][1000 genomes]
rs73778394	0.87[AFR][1000 genomes]
rs73779112	0.89[AFR][1000 genomes]
rs73781924	0.89[AFR][1000 genomes]
rs7725708	0.85[AFR][1000 genomes]
rs7734904	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7735425	0.88[EUR][1000 genomes]
rs919771	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][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	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

No data

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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