Variant report

Variant	rs56116089
Chromosome Location	chr13:52962369-52962370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs55645852	1.00[AFR][1000 genomes]
rs55796806	0.88[AFR][1000 genomes]
rs55924773	1.00[AFR][1000 genomes]
rs56252739	1.00[AFR][1000 genomes]
rs56758534	0.89[AFR][1000 genomes]
rs57339165	0.88[AFR][1000 genomes]
rs57461595	0.88[AFR][1000 genomes]
rs60539260	0.82[AFR][1000 genomes]
rs60864284	1.00[AFR][1000 genomes]
rs61285838	0.88[AFR][1000 genomes]
rs74085735	0.88[AFR][1000 genomes]
rs74085745	1.00[AFR][1000 genomes]
rs74085746	1.00[AFR][1000 genomes]
rs74085748	1.00[AFR][1000 genomes]
rs74085750	1.00[AFR][1000 genomes]
rs74085767	1.00[AFR][1000 genomes]
rs74085773	0.89[AFR][1000 genomes]
rs74085776	1.00[AFR][1000 genomes]
rs74085781	1.00[AFR][1000 genomes]
rs74085783	0.88[AFR][1000 genomes]
rs74087342	0.88[AFR][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	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52946000-52969600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr13:52946200-52979200	Weak transcription	A549	lung
3	chr13:52947800-52968000	Weak transcription	NHDF-Ad	bronchial
4	chr13:52949800-52979000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:52952000-52964400	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:52952600-52963400	Weak transcription	Fetal Intestine Large	intestine
7	chr13:52952600-52969200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:52952800-52967000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:52952800-52968000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr13:52952800-52969000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:52952800-52969200	Weak transcription	Fetal Brain Female	brain
12	chr13:52952800-52969200	Weak transcription	Spleen	Spleen
13	chr13:52952800-52969200	Weak transcription	NHEK	skin
14	chr13:52952800-52969600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:52952800-52969600	Weak transcription	NHLF	lung
16	chr13:52952800-52971400	Weak transcription	Right Ventricle	heart
17	chr13:52953000-52964400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr13:52953000-52968000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:52953000-52970000	Weak transcription	Ovary	ovary
20	chr13:52955600-52969600	Weak transcription	Lung	lung
21	chr13:52956200-52978200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:52957400-52967000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr13:52957800-52969000	Weak transcription	Adipose Nuclei	Adipose
24	chr13:52957800-52969600	Weak transcription	Fetal Stomach	stomach
25	chr13:52958000-52969200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:52958000-52969200	Weak transcription	HSMMtube	muscle
27	chr13:52958000-52969400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr13:52958000-52970800	Weak transcription	Fetal Lung	lung
29	chr13:52960200-52962600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:52960400-52962800	Weak transcription	HSMM	muscle
31	chr13:52960400-52964000	Weak transcription	HMEC	breast
32	chr13:52960400-52964400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:52960800-52969000	Weak transcription	Osteobl	bone
34	chr13:52961000-52964400	Weak transcription	Fetal Muscle Leg	muscle
35	chr13:52961000-52964600	Weak transcription	HUVEC	blood vessel
36	chr13:52961000-52968000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr13:52961200-52969000	Weak transcription	Right Atrium	heart
38	chr13:52961400-52964400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr13:52961400-52967800	Weak transcription	Brain Anterior Caudate	brain
40	chr13:52961400-52969000	Weak transcription	Left Ventricle	heart
41	chr13:52961400-52969200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr13:52961800-52963800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:52962000-52963200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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