Variant report

Variant	rs58654116
Chromosome Location	chr1:92626938-92626939
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:6)

rs_ID	r²[population]
rs57646033	0.84[AFR][1000 genomes]
rs60274844	0.84[AFR][1000 genomes]
rs6690811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72956885	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72956889	1.00[AMR][1000 genomes]
rs72956894	1.00[AMR][1000 genomes]

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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv871415	chr1:92340684-92641607	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv871144	chr1:92380302-92641607	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv546821	chr1:92525678-92650349	ZNF genes & repeats Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92601200-92634400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:92609800-92651200	Weak transcription	Fetal Kidney	kidney
3	chr1:92613400-92645400	Weak transcription	Gastric	stomach
4	chr1:92614000-92627600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:92615600-92646000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:92620600-92634400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:92620600-92646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:92620800-92633400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:92620800-92645800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:92621000-92646800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:92622400-92628000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:92625000-92646800	Weak transcription	Pancreas	Pancrea
13	chr1:92625000-92648200	Weak transcription	Fetal Stomach	stomach
14	chr1:92625400-92627600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:92625400-92642600	Weak transcription	Fetal Lung	lung
16	chr1:92625600-92651000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:92625800-92628200	Strong transcription	Brain Cingulate Gyrus	brain
18	chr1:92626000-92628200	Strong transcription	Ovary	ovary
19	chr1:92626200-92629600	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:92626200-92642600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:92626200-92646000	Weak transcription	Psoas Muscle	Psoas
22	chr1:92626200-92652000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:92626400-92627600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:92626400-92627600	Weak transcription	Left Ventricle	heart
25	chr1:92626400-92628200	Strong transcription	Adipose Nuclei	Adipose
26	chr1:92626400-92632600	Weak transcription	Fetal Brain Male	brain
27	chr1:92626400-92634400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:92626400-92643000	Weak transcription	Fetal Intestine Large	intestine
29	chr1:92626400-92644200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:92626600-92627600	Weak transcription	Aorta	Aorta
31	chr1:92626600-92627600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:92626600-92627600	Weak transcription	Lung	lung
33	chr1:92626600-92627800	Weak transcription	Dnd41	blood
34	chr1:92626600-92633000	Weak transcription	Fetal Brain Female	brain
35	chr1:92626600-92634200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:92626600-92634200	Weak transcription	Brain Germinal Matrix	brain
37	chr1:92626600-92634400	Weak transcription	Brain Angular Gyrus	brain
38	chr1:92626600-92644000	Weak transcription	Liver	Liver
39	chr1:92626600-92648400	Weak transcription	Fetal Intestine Small	intestine
40	chr1:92626600-92650800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:92626600-92657400	Weak transcription	Right Ventricle	heart
42	chr1:92626800-92627200	Weak transcription	Spleen	Spleen
43	chr1:92626800-92627600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:92626800-92627600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:92626800-92630800	Weak transcription	Thymus	Thymus
46	chr1:92626800-92634400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:92626800-92646600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:92626800-92650000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:92626800-92651400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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