Variant report

Variant	rs58762652
Chromosome Location	chr3:51631070-51631071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12485610	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12486568	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487426	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12490471	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12492624	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12493265	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493618	0.81[EUR][1000 genomes]
rs12493857	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12494462	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12496340	0.93[EUR][1000 genomes]
rs13089799	0.87[EUR][1000 genomes]
rs13090348	0.87[EUR][1000 genomes]
rs13324384	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17051811	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2033703	0.87[EUR][1000 genomes]
rs2082992	1.00[EUR][1000 genomes]
rs2082993	1.00[EUR][1000 genomes]
rs2356298	0.81[ASN][1000 genomes]
rs35536327	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687553	1.00[EUR][1000 genomes]
rs4687563	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687592	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687599	0.87[EUR][1000 genomes]
rs4687605	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687656	1.00[EUR][1000 genomes]
rs4687691	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687769	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4687794	1.00[EUR][1000 genomes]
rs55667499	1.00[EUR][1000 genomes]
rs55706150	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55872019	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56239081	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56729479	0.81[ASN][1000 genomes]
rs57027950	0.87[EUR][1000 genomes]
rs58059174	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58189274	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59564034	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59838596	0.87[EUR][1000 genomes]
rs60007226	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60606339	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61233013	0.83[ASN][1000 genomes]
rs61689323	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72951443	1.00[EUR][1000 genomes]
rs72951490	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7375146	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73834253	0.87[EUR][1000 genomes]
rs73834254	0.87[EUR][1000 genomes]
rs73834258	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73834265	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9827186	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9842600	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9843583	0.94[EUR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3414786	chr3:51628711-51632506	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51588000-51640000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:51600800-51654600	Weak transcription	Stomach Mucosa	stomach
3	chr3:51601200-51640000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:51602800-51643800	Weak transcription	Right Atrium	heart
5	chr3:51613200-51640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:51613400-51643600	Weak transcription	Pancreas	Pancrea
7	chr3:51616600-51640200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:51619600-51631600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:51622600-51633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:51622800-51631600	Strong transcription	Liver	Liver
11	chr3:51623000-51633000	Strong transcription	Primary T cells from cord blood	blood
12	chr3:51623200-51639800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:51623400-51631600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:51623800-51631800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:51624200-51631600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:51624400-51631800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:51625200-51631800	Weak transcription	NHLF	lung
18	chr3:51625200-51639400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:51625200-51640000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:51625200-51655400	Weak transcription	Gastric	stomach
21	chr3:51625400-51637400	Weak transcription	HMEC	breast
22	chr3:51625400-51640200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:51625400-51641000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:51625400-51642200	Weak transcription	Brain Germinal Matrix	brain
25	chr3:51625400-51663400	Weak transcription	Right Ventricle	heart
26	chr3:51625600-51631400	Weak transcription	Fetal Heart	heart
27	chr3:51625600-51631800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:51625600-51639800	Weak transcription	Thymus	Thymus
29	chr3:51625600-51642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:51625600-51643400	Weak transcription	Esophagus	oesophagus
31	chr3:51625600-51654000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:51625600-51654000	Weak transcription	Ovary	ovary
33	chr3:51625600-51655400	Weak transcription	Aorta	Aorta
34	chr3:51625600-51658200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:51625800-51636400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:51625800-51642000	Weak transcription	HSMMtube	muscle
37	chr3:51625800-51642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:51625800-51645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:51625800-51647000	Weak transcription	Fetal Brain Female	brain
40	chr3:51625800-51651000	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:51625800-51654000	Weak transcription	Left Ventricle	heart
42	chr3:51625800-51655200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:51625800-51655400	Weak transcription	Lung	lung
44	chr3:51625800-51655800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:51626000-51632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:51626000-51632200	Weak transcription	HUVEC	blood vessel
47	chr3:51626000-51640400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:51626000-51640400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:51626000-51651400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:51626000-51654600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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