Variant report

Variant	rs11953486
Chromosome Location	chr5:108280436-108280437
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs11948881	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11949066	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11949367	0.86[EUR][1000 genomes]
rs11949510	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11949619	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11949648	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11949706	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11951971	0.88[EUR][1000 genomes]
rs11951974	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11952227	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11952572	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11953136	0.88[EUR][1000 genomes]
rs11953198	0.80[EUR][1000 genomes]
rs11954716	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11954988	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11955886	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11956908	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11957358	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11958918	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11959492	0.89[EUR][1000 genomes]
rs11959577	0.85[EUR][1000 genomes]
rs11959681	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11960713	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12153527	0.87[YRI][hapmap]
rs17534354	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs17534396	0.82[YRI][hapmap]
rs34412145	0.88[EUR][1000 genomes]
rs34679271	0.80[EUR][1000 genomes]
rs3851457	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3851458	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56134914	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56381733	0.84[EUR][1000 genomes]
rs57158292	0.80[EUR][1000 genomes]
rs57404758	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57622369	0.86[EUR][1000 genomes]
rs59055229	0.84[EUR][1000 genomes]
rs59216020	0.88[EUR][1000 genomes]
rs60946864	0.88[EUR][1000 genomes]
rs66485253	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66834040	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67156774	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67338203	0.84[EUR][1000 genomes]
rs72787096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72787098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72787099	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72787100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72787101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72787102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789304	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789305	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72789306	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789307	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789312	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72789313	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72789315	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72789316	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789319	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789320	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72789326	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789332	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789333	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72789335	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789341	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789345	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789347	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789348	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789350	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789352	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72790510	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72790512	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72790514	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72790515	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72790520	0.89[EUR][1000 genomes]
rs72790521	0.89[EUR][1000 genomes]
rs72790524	0.88[EUR][1000 genomes]
rs72790525	0.88[EUR][1000 genomes]
rs72790528	0.88[EUR][1000 genomes]
rs72790529	0.88[EUR][1000 genomes]
rs72790530	0.88[EUR][1000 genomes]
rs72790538	0.88[EUR][1000 genomes]
rs72790539	0.88[EUR][1000 genomes]
rs72790542	0.88[EUR][1000 genomes]
rs72790545	0.88[EUR][1000 genomes]
rs72790546	0.88[EUR][1000 genomes]
rs72790548	0.85[EUR][1000 genomes]
rs72790551	0.88[EUR][1000 genomes]
rs72790552	0.88[EUR][1000 genomes]
rs72790559	0.85[EUR][1000 genomes]
rs72790562	0.86[EUR][1000 genomes]
rs72790565	0.86[EUR][1000 genomes]
rs72790567	0.86[EUR][1000 genomes]
rs72790568	0.86[EUR][1000 genomes]
rs72790574	0.86[EUR][1000 genomes]
rs72790577	0.86[EUR][1000 genomes]
rs72790579	0.86[EUR][1000 genomes]
rs72792001	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72793903	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72793905	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793906	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793909	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72793918	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72793920	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72793922	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72793923	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72793926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72793927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72793930	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72793933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73209329	0.81[AMR][1000 genomes]
rs73209347	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7713828	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7723264	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7723604	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7723644	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7734904	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7735425	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7736915	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs919771	0.84[CEU][hapmap];0.83[EUR][1000 genomes]

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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
3	chr5:108221400-108280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:108230200-108302400	Weak transcription	HSMM	muscle
5	chr5:108244200-108295000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:108254000-108311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:108268200-108280800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:108268400-108301400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:108270600-108289200	Weak transcription	K562	blood
10	chr5:108277600-108283800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:108277600-108322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:108278000-108308200	Weak transcription	Fetal Kidney	kidney
13	chr5:108278800-108280800	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:108279000-108295000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:108279200-108281000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:108279200-108302600	Weak transcription	Ovary	ovary
17	chr5:108279200-108325600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:108279400-108285200	Weak transcription	Fetal Lung	lung
19	chr5:108279600-108280800	Weak transcription	Brain Angular Gyrus	brain
20	chr5:108279800-108284000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:108279800-108295200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:108280200-108281200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:108280200-108282800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr5:108280400-108282000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr5:108280400-108283400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr5:108280400-108283400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr5:108280400-108286000	Enhancers	HUES48 Cell Line	embryonic stem cell

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