Variant report

Variant	rs11980940
Chromosome Location	chr7:79033194-79033195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10214949	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10224707	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs10239869	0.82[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs10248625	0.81[ASN][1000 genomes]
rs10262779	0.81[ASN][1000 genomes]
rs10485953	0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs10485956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11976160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11976606	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs12706162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13222501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13228109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13231892	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13239510	0.80[ASN][1000 genomes]
rs17152429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17152446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190181	0.80[ASN][1000 genomes]
rs2190182	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs2214808	0.91[JPT][hapmap]
rs2364920	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs28681068	0.80[ASN][1000 genomes]
rs2886214	0.80[ASN][1000 genomes]
rs34405085	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34931968	0.94[ASN][1000 genomes]
rs35831489	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36004335	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4236606	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4236607	0.81[ASN][1000 genomes]
rs4291207	0.81[ASN][1000 genomes]
rs4559162	0.80[ASN][1000 genomes]
rs4730807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4730814	0.80[ASN][1000 genomes]
rs4730815	0.80[ASN][1000 genomes]
rs4730816	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4730818	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4730820	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs57524293	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59843089	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6466639	0.90[JPT][hapmap]
rs6466640	0.82[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs6953480	0.80[ASN][1000 genomes]
rs6953613	0.80[ASN][1000 genomes]
rs7791179	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7791667	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs7803949	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs848936	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv888514	chr7:78987060-79061837	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv607664	chr7:78998409-79057761	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv607665	chr7:79027730-79063644	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv607666	chr7:79029872-79063644	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv607667	chr7:79029872-79065268	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv607668	chr7:79029872-79070452	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79027800-79033200	Weak transcription	NHDF-Ad	bronchial
2	chr7:79028000-79033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:79028000-79033200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:79028000-79034600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:79029800-79036400	Enhancers	Liver	Liver
6	chr7:79030800-79034800	Weak transcription	Brain Substantia Nigra	brain
7	chr7:79030800-79036800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:79031000-79033200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:79031000-79033200	Weak transcription	Brain Angular Gyrus	brain
10	chr7:79031000-79034800	Weak transcription	Adipose Nuclei	Adipose
11	chr7:79031000-79040800	Weak transcription	Brain Anterior Caudate	brain
12	chr7:79032200-79033400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:79032200-79033600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:79032200-79033600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:79032200-79033600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:79032200-79033600	Enhancers	Osteobl	bone
17	chr7:79032200-79033800	Enhancers	NHLF	lung
18	chr7:79032400-79033800	Enhancers	Fetal Lung	lung
19	chr7:79032600-79033600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:79033000-79033400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:79033000-79035000	Enhancers	Brain Hippocampus Middle	brain

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