Variant report

Variant	rs9824541
Chromosome Location	chr3:61552375-61552376
allele	G/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:13)

rs_ID	r²[population]
rs1574016	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17669146	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1878772	1.00[ASN][1000 genomes]
rs2886519	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6445221	0.87[AFR][1000 genomes]
rs6445222	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6445224	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636186	0.98[ASN][1000 genomes]
rs9808938	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821236	0.91[ASN][1000 genomes]
rs9827952	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840322	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9845678	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61549800-61553000	Weak transcription	Small Intestine	intestine
2	chr3:61550200-61552600	Enhancers	HepG2	liver
3	chr3:61550400-61554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:61550600-61568600	Weak transcription	Pancreas	Pancrea
5	chr3:61550800-61552400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:61550800-61552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:61550800-61555400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:61550800-61556800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:61550800-61556800	Weak transcription	Ovary	ovary
10	chr3:61550800-61557600	Weak transcription	Psoas Muscle	Psoas
11	chr3:61550800-61558400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:61550800-61574200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:61551000-61552400	Weak transcription	Liver	Liver
14	chr3:61551000-61552600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:61551000-61552800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:61551000-61552800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:61551000-61554800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:61551000-61555800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:61551000-61556800	Weak transcription	NH-A	brain
20	chr3:61551000-61557400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:61551000-61557600	Weak transcription	Aorta	Aorta
22	chr3:61551000-61557600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:61551000-61557600	Weak transcription	Right Atrium	heart
24	chr3:61551000-61559800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:61551000-61559800	Weak transcription	NHEK	skin
26	chr3:61551000-61561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:61551200-61552400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:61551200-61555600	Weak transcription	Fetal Lung	lung
29	chr3:61551200-61555800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:61551200-61556400	Weak transcription	Fetal Brain Male	brain
31	chr3:61551200-61557600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:61551200-61560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:61551400-61555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:61551400-61555800	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:61551600-61553000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:61551600-61554800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:61551600-61554800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:61551600-61555400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:61551600-61556800	Weak transcription	Right Ventricle	heart
40	chr3:61551600-61557600	Weak transcription	Fetal Kidney	kidney
41	chr3:61551600-61559800	Weak transcription	NHLF	lung
42	chr3:61551600-61563800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:61551800-61555200	Weak transcription	Brain Angular Gyrus	brain
44	chr3:61551800-61555600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:61551800-61556200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:61552000-61552400	Weak transcription	Adipose Nuclei	Adipose
47	chr3:61552000-61552600	Enhancers	Left Ventricle	heart
48	chr3:61552000-61553000	Weak transcription	Fetal Heart	heart
49	chr3:61552000-61553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:61552000-61554800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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