Variant report

Variant	rs58646564
Chromosome Location	chr13:49941780-49941781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs56344326	1.00[AMR][1000 genomes]
rs60549375	1.00[AMR][1000 genomes]
rs60948185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61063436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072521	1.00[AMR][1000 genomes]
rs74072523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072537	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49889000-49944600	Weak transcription	Brain Angular Gyrus	brain
2	chr13:49889000-49947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:49889200-49944600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr13:49912600-49948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:49922400-49946600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:49922400-49947800	Weak transcription	Right Ventricle	heart
7	chr13:49922800-49951400	Weak transcription	Gastric	stomach
8	chr13:49923200-49951200	Weak transcription	Pancreas	Pancrea
9	chr13:49929400-49950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:49932200-49941800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:49932200-49944600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:49934200-49942600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:49934200-49957400	Weak transcription	Left Ventricle	heart
14	chr13:49937800-49942200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr13:49938600-49961000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:49940800-49942000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr13:49941000-49942200	Enhancers	Stomach Smooth Muscle	stomach
18	chr13:49941000-49943000	Enhancers	Colon Smooth Muscle	Colon
19	chr13:49941200-49942000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr13:49941200-49942200	Weak transcription	Aorta	Aorta
21	chr13:49941200-49942400	Enhancers	Adipose Nuclei	Adipose
22	chr13:49941200-49942600	Enhancers	NHDF-Ad	bronchial
23	chr13:49941200-49943600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr13:49941400-49942400	Enhancers	Fetal Heart	heart
25	chr13:49941400-49942600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:49941400-49942800	Enhancers	Brain Hippocampus Middle	brain
27	chr13:49941600-49941800	Enhancers	NH-A	brain
28	chr13:49941600-49942400	Weak transcription	NHLF	lung
29	chr13:49941600-49943000	Enhancers	Ovary	ovary
30	chr13:49941600-49944400	Weak transcription	Brain Anterior Caudate	brain
31	chr13:49941600-49946200	Weak transcription	HSMMtube	muscle

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