Variant report

Variant	rs16824913
Chromosome Location	chr3:116162235-116162236
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13094055	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316464	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16824908	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920175	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1920197	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35192256	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35220064	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289053	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875727	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881385	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757886	chr3:116142130-116307542	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759171	chr3:116142130-116307542	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116159000-116163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:116160400-116165000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:116160600-116165200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:116160800-116162600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:116160800-116164600	Active TSS	Brain Hippocampus Middle	brain
6	chr3:116161000-116163200	Active TSS	Stomach Smooth Muscle	stomach
7	chr3:116161000-116164000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:116161000-116164600	Active TSS	Rectal Smooth Muscle	rectum
9	chr3:116161000-116164800	Active TSS	Fetal Brain Female	brain
10	chr3:116161000-116165200	Active TSS	Brain Substantia Nigra	brain
11	chr3:116161200-116163000	Active TSS	Brain Anterior Caudate	brain
12	chr3:116161200-116164600	Active TSS	Brain Angular Gyrus	brain
13	chr3:116161200-116164600	Active TSS	Colon Smooth Muscle	Colon
14	chr3:116161400-116162400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:116161400-116162600	Active TSS	Brain Germinal Matrix	brain
16	chr3:116161400-116163200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:116161400-116164400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:116161400-116164600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:116161600-116162600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:116161600-116164600	Active TSS	Fetal Stomach	stomach
21	chr3:116161600-116164800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:116161800-116162400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:116162000-116162400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
24	chr3:116162000-116162400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:116162000-116162400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:116162000-116162400	Flanking Active TSS	Fetal Brain Male	brain
27	chr3:116162000-116162400	Flanking Active TSS	NH-A	brain
28	chr3:116162000-116162600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:116162000-116163600	Active TSS	Fetal Muscle Leg	muscle
30	chr3:116162000-116164200	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr3:116162200-116162400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr3:116162200-116162400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr3:116162200-116162400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:116162200-116162400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr3:116162200-116162400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:116162200-116162400	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr3:116162200-116162400	Flanking Active TSS	Fetal Kidney	kidney
38	chr3:116162200-116162600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
39	chr3:116162200-116162600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:116162200-116162600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
41	chr3:116162200-116162600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:116162200-116162600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:116162200-116162600	Active TSS	NHDF-Ad	bronchial
44	chr3:116162200-116162800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:116162200-116163000	Active TSS	Fetal Lung	lung
46	chr3:116162200-116163200	Active TSS	Fetal Intestine Small	intestine
47	chr3:116162200-116163600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:116162200-116163600	Active TSS	Fetal Muscle Trunk	muscle
49	chr3:116162200-116164400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:116162200-116164400	Active TSS	NHLF	lung

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