Variant report

Variant	rs5000757
Chromosome Location	chr3:120165292-120165293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1147706	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1147709	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1147710	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1147712	0.82[ASN][1000 genomes]
rs1147714	0.82[ASN][1000 genomes]
rs1147715	0.82[ASN][1000 genomes]
rs1147716	0.82[ASN][1000 genomes]
rs1259309	0.82[ASN][1000 genomes]
rs1259311	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1259312	0.82[ASN][1000 genomes]
rs1259329	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259331	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259332	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259334	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259336	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259337	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259338	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259456	0.82[ASN][1000 genomes]
rs1259471	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259472	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259473	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1262395	0.82[ASN][1000 genomes]
rs1267675	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1267693	0.81[ASN][1000 genomes]
rs1270209	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1520881	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1716835	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1716837	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1733296	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1733298	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1733299	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1733301	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733303	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733304	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733306	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733307	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733319	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2700262	0.82[ASN][1000 genomes]
rs2702155	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6768839	0.83[EUR][1000 genomes]
rs735138	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs874477	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs874478	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874479	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874480	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9631455	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3499188	chr3:120160412-120166010	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv436396	chr3:120160617-120166439	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3499192	chr3:120160812-120165910	Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3499191	chr3:120161046-120165383	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3324710	chr3:120161962-120166460	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:120138200-120169200	Weak transcription	Gastric	stomach
3	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
5	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:120153000-120167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:120155800-120168400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120156200-120166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:120156600-120168800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:120156800-120166000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:120158000-120166200	Weak transcription	Fetal Brain Female	brain
12	chr3:120158000-120167600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:120158200-120167400	Weak transcription	Brain Germinal Matrix	brain
14	chr3:120158400-120165600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:120158800-120166000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:120158800-120167400	Weak transcription	A549	lung
17	chr3:120159600-120165800	Weak transcription	Spleen	Spleen
18	chr3:120160000-120167400	Weak transcription	HMEC	breast
19	chr3:120160000-120167600	Weak transcription	NHEK	skin
20	chr3:120160400-120165800	Weak transcription	Placenta	Placenta
21	chr3:120160600-120165800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:120160600-120166000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:120160600-120167400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:120160800-120166000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:120160800-120166000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:120160800-120166200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:120160800-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:120160800-120167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:120161000-120165400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:120161000-120166000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:120161000-120167400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:120161200-120166000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:120161200-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:120161400-120165800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:120162200-120165800	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr3:120162200-120166800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:120162200-120166800	Genic enhancers	NH-A	brain
38	chr3:120162200-120168800	Weak transcription	Esophagus	oesophagus
39	chr3:120162400-120165400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:120162600-120165800	Weak transcription	Fetal Brain Male	brain
41	chr3:120162800-120166000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:120163000-120169000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:120163200-120165400	Weak transcription	Fetal Kidney	kidney
44	chr3:120163200-120166400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:120163400-120165600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:120163800-120165800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:120163800-120166000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:120163800-120166600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
49	chr3:120163800-120167800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:120164600-120165800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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