Variant report

Variant	rs59753245
Chromosome Location	chr3:112085046-112085047
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs4339085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57654125	0.95[AFR][1000 genomes]
rs58693268	1.00[ASN][1000 genomes]
rs59910010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61563653	0.95[AFR][1000 genomes]
rs6780859	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6781162	0.92[AFR][1000 genomes]
rs6784174	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6791181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6797023	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6807033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6807758	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6807853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6807944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72952427	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72952431	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72952432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72952434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72952435	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72952441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7645214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	esv2547495	chr3:112084576-112086011	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:112070200-112086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:112070600-112086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:112070600-112088800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:112070800-112090600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:112077200-112094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:112077600-112107200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:112077800-112085400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:112077800-112085400	Weak transcription	Ovary	ovary
11	chr3:112078000-112085200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:112078200-112086400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:112079400-112085600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:112079400-112085800	Strong transcription	Primary hematopoietic stem cells	blood
15	chr3:112079400-112086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:112079600-112085800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:112080000-112088800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:112080000-112096000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:112080600-112087400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:112081000-112085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:112081000-112088800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:112081200-112085400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:112081200-112085800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:112081200-112092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:112081400-112085400	Weak transcription	Fetal Brain Male	brain
26	chr3:112081400-112088000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:112081400-112091600	Weak transcription	Primary T cells from cord blood	blood
28	chr3:112082200-112096000	Weak transcription	Fetal Stomach	stomach
29	chr3:112082600-112094600	Weak transcription	Brain Anterior Caudate	brain
30	chr3:112083000-112085600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:112083000-112085600	Enhancers	HMEC	breast
32	chr3:112083200-112085800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:112083200-112086000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:112083400-112085400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:112083400-112086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:112083400-112092200	Weak transcription	Primary B cells from cord blood	blood
37	chr3:112083600-112085400	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr3:112083600-112085600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:112083600-112085800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:112083800-112085400	Weak transcription	Brain Substantia Nigra	brain
41	chr3:112083800-112085800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:112083800-112086200	Strong transcription	Fetal Thymus	thymus
43	chr3:112083800-112090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:112083800-112092200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:112084000-112085400	Genic enhancers	GM12878-XiMat	blood
46	chr3:112084000-112085800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:112084000-112085800	Strong transcription	Fetal Brain Female	brain
48	chr3:112084000-112087200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:112084000-112090600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:112084000-112094800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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