Variant report

Variant	rs61563653
Chromosome Location	chr3:112092519-112092520
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs4339085	0.95[AFR][1000 genomes]
rs56980412	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57654125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57814913	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59514600	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59753245	0.95[AFR][1000 genomes]
rs59895987	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59910010	0.95[AFR][1000 genomes]
rs60112764	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6780859	0.88[AFR][1000 genomes]
rs6781162	0.88[AFR][1000 genomes]
rs6784174	0.90[AFR][1000 genomes]
rs6791181	0.95[AFR][1000 genomes]
rs6794784	0.95[AFR][1000 genomes]
rs6797023	0.90[AFR][1000 genomes]
rs6807033	0.95[AFR][1000 genomes]
rs6807758	0.86[AFR][1000 genomes]
rs6807853	0.90[AFR][1000 genomes]
rs6807944	0.90[AFR][1000 genomes]
rs72952427	0.86[AFR][1000 genomes]
rs72952431	0.90[AFR][1000 genomes]
rs72952432	0.90[AFR][1000 genomes]
rs72952434	0.95[AFR][1000 genomes]
rs72952435	0.90[AFR][1000 genomes]
rs72952441	0.95[AFR][1000 genomes]
rs72952461	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72952465	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7645214	0.95[AFR][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	nsv877341	chr3:112079277-112125521	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1002567	chr3:112088498-112144063	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2830128	chr3:112090292-112144026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:112077200-112094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:112077600-112107200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:112080000-112096000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:112081200-112092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:112082200-112096000	Weak transcription	Fetal Stomach	stomach
7	chr3:112082600-112094600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:112084000-112094800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:112084200-112092600	Weak transcription	Fetal Kidney	kidney
10	chr3:112084600-112093200	Weak transcription	Fetal Lung	lung
11	chr3:112084800-112096000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:112084800-112096800	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:112085000-112095600	Weak transcription	Thymus	Thymus
14	chr3:112085400-112096000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:112085600-112095400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:112085600-112096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:112085800-112096400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:112085800-112096600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:112085800-112101400	Weak transcription	Aorta	Aorta
20	chr3:112086000-112095000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:112086000-112095600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:112087600-112096400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:112088200-112092800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:112090400-112092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:112090600-112093000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr3:112090600-112093600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:112091200-112092800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:112091400-112093200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr3:112091400-112098400	Enhancers	Adipose Nuclei	Adipose
30	chr3:112091600-112092600	Enhancers	Primary T cells from cord blood	blood
31	chr3:112091600-112093000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:112091600-112095600	Enhancers	Placenta	Placenta
33	chr3:112091800-112092800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:112092000-112093000	Enhancers	Primary B cells from peripheral blood	blood
35	chr3:112092000-112093200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:112092000-112093200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:112092200-112092600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:112092200-112092600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:112092200-112092800	Enhancers	Primary B cells from cord blood	blood
40	chr3:112092200-112093000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:112092200-112093200	Enhancers	Fetal Thymus	thymus
42	chr3:112092200-112093400	Enhancers	Primary hematopoietic stem cells	blood
43	chr3:112092400-112092800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:112092400-112093000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:112092400-112094400	Weak transcription	Left Ventricle	heart

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