Variant report

Variant	rs11960608
Chromosome Location	chr5:92872156-92872157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11135388	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951859	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11952115	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952600	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187239	0.93[EUR][1000 genomes]
rs12188845	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12188905	0.90[EUR][1000 genomes]
rs1370977	0.89[EUR][1000 genomes]
rs1457101	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082127	0.91[EUR][1000 genomes]
rs17082129	0.91[EUR][1000 genomes]
rs17083145	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17083155	0.86[EUR][1000 genomes]
rs17083181	0.91[EUR][1000 genomes]
rs17083191	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17083194	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17083198	0.91[EUR][1000 genomes]
rs17083200	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17083213	0.93[EUR][1000 genomes]
rs17083228	0.91[EUR][1000 genomes]
rs1824153	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1844343	0.91[EUR][1000 genomes]
rs2083227	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2344387	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55861967	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57165666	0.89[EUR][1000 genomes]
rs57690257	0.91[EUR][1000 genomes]
rs59360932	0.93[EUR][1000 genomes]
rs61324921	0.91[EUR][1000 genomes]
rs61352323	0.93[EUR][1000 genomes]
rs6556823	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6556824	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6556826	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866771	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6879816	0.93[EUR][1000 genomes]
rs6880843	0.89[EUR][1000 genomes]
rs6889857	0.84[EUR][1000 genomes]
rs73133214	0.89[EUR][1000 genomes]
rs73133217	0.89[EUR][1000 genomes]
rs73133226	0.89[EUR][1000 genomes]
rs73133228	0.89[EUR][1000 genomes]
rs73133239	0.91[EUR][1000 genomes]
rs73133251	0.91[EUR][1000 genomes]
rs73133254	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73133258	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133261	0.91[EUR][1000 genomes]
rs73133265	0.90[EUR][1000 genomes]
rs73133275	0.91[EUR][1000 genomes]
rs73133278	0.91[EUR][1000 genomes]
rs73133280	0.91[EUR][1000 genomes]
rs73133282	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73133283	0.93[EUR][1000 genomes]
rs73133287	0.93[EUR][1000 genomes]
rs73133289	0.83[EUR][1000 genomes]
rs73133292	0.82[EUR][1000 genomes]
rs73133301	0.89[EUR][1000 genomes]
rs73135313	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73772907	0.89[EUR][1000 genomes]
rs7712899	0.89[EUR][1000 genomes]
rs7715034	0.89[EUR][1000 genomes]
rs7727107	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022355	chr5:92846496-92911797	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
2	nsv537807	chr5:92846496-92911797	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
3	nsv882382	chr5:92853645-92891029	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	lncRNA	8 gene(s)	inside rSNPs	n/a
4	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92856800-92887200	Weak transcription	HUVEC	blood vessel
2	chr5:92857800-92872200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:92859200-92905000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:92859400-92905000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:92859400-92905600	Weak transcription	Placenta	Placenta
6	chr5:92859600-92872400	Weak transcription	Fetal Stomach	stomach
7	chr5:92859600-92900400	Weak transcription	Fetal Intestine Small	intestine
8	chr5:92860000-92908000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:92860400-92880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:92862800-92887800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:92866400-92875200	Weak transcription	Esophagus	oesophagus
12	chr5:92867200-92888800	Weak transcription	Ovary	ovary
13	chr5:92868400-92880200	Weak transcription	Fetal Intestine Large	intestine
14	chr5:92868400-92881400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:92868400-92882800	Weak transcription	Fetal Brain Male	brain
16	chr5:92868600-92872200	Weak transcription	Fetal Brain Female	brain
17	chr5:92868600-92872400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:92868600-92872400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:92868600-92872600	Weak transcription	HSMM	muscle
20	chr5:92868600-92874400	Weak transcription	NH-A	brain
21	chr5:92868600-92900200	Weak transcription	Hela-S3	cervix
22	chr5:92868800-92872200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:92868800-92873600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:92868800-92877200	Weak transcription	Osteobl	bone
25	chr5:92868800-92881600	Weak transcription	NHLF	lung
26	chr5:92868800-92887800	Weak transcription	NHDF-Ad	bronchial
27	chr5:92869000-92881000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:92870200-92872800	Strong transcription	Fetal Kidney	kidney
29	chr5:92871400-92873800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:92871800-92872600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:92872000-92872400	ZNF genes & repeats	Adipose Nuclei	Adipose
32	chr5:92872000-92872800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:92872000-92874800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr5:92872000-92881000	Strong transcription	Fetal Lung	lung

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