Variant report

Variant	rs56772417
Chromosome Location	chr3:113097809-113097810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10511325	0.82[ASN][1000 genomes]
rs11917149	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11917288	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11919330	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11920725	0.82[ASN][1000 genomes]
rs11922838	0.82[ASN][1000 genomes]
rs11923128	0.82[ASN][1000 genomes]
rs11924109	0.91[EUR][1000 genomes]
rs11926687	0.82[ASN][1000 genomes]
rs1463639	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1513288	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16845109	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16860770	1.00[AFR][1000 genomes]
rs16860962	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16861014	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16861023	0.82[ASN][1000 genomes]
rs16861025	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16861032	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16861045	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16861077	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16861109	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17255950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17256551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17256752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17320040	1.00[AFR][1000 genomes]
rs17322613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17325024	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1906141	0.82[ASN][1000 genomes]
rs1989359	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2129431	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2129432	0.82[ASN][1000 genomes]
rs2271496	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2291412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306068	0.91[EUR][1000 genomes]
rs2306070	0.91[EUR][1000 genomes]
rs28472841	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34600669	1.00[AFR][1000 genomes]
rs35758075	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35812463	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41271353	1.00[AFR][1000 genomes]
rs56685963	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57104308	1.00[AFR][1000 genomes]
rs57115529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57164268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57366942	0.82[ASN][1000 genomes]
rs58905600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58988763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59271111	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59493419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59673391	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59742486	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs60582065	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60697865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60940543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61065093	0.91[EUR][1000 genomes]
rs61575357	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61594119	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6438150	0.82[ASN][1000 genomes]
rs6438151	0.82[ASN][1000 genomes]
rs6783691	0.91[EUR][1000 genomes]
rs735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7610552	0.82[ASN][1000 genomes]
rs7635203	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs998647	1.00[AFR][1000 genomes]
rs999365	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:113066200-113102800	Weak transcription	Aorta	Aorta
4	chr3:113066400-113099000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:113066400-113117600	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:113068400-113117000	Weak transcription	Thymus	Thymus
7	chr3:113069000-113101800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:113070600-113099000	Weak transcription	Adipose Nuclei	Adipose
9	chr3:113072400-113117200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
11	chr3:113077800-113102400	Weak transcription	HSMM	muscle
12	chr3:113078600-113109800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:113080000-113114200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:113080200-113117600	Weak transcription	Psoas Muscle	Psoas
16	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:113081600-113099000	Weak transcription	Left Ventricle	heart
18	chr3:113081600-113103400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:113081600-113104400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:113081600-113105600	Weak transcription	Esophagus	oesophagus
21	chr3:113081600-113105800	Weak transcription	Gastric	stomach
22	chr3:113081600-113106200	Weak transcription	Lung	lung
23	chr3:113081600-113121200	Weak transcription	Ovary	ovary
24	chr3:113081600-113121200	Weak transcription	Pancreas	Pancrea
25	chr3:113081800-113099000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:113081800-113116600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:113082200-113113200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:113086200-113105800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:113086200-113106400	Weak transcription	Fetal Stomach	stomach
30	chr3:113090800-113106600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:113090800-113121200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:113091800-113104600	Weak transcription	NH-A	brain
33	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
34	chr3:113093000-113098400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:113093000-113099400	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:113094200-113108800	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:113096200-113100600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:113096200-113105600	Weak transcription	Liver	Liver
40	chr3:113096400-113106600	Weak transcription	GM12878-XiMat	blood
41	chr3:113096600-113121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:113096800-113099800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:113097400-113099000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:113097400-113099400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:113097400-113101800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:113097600-113100000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:113097600-113103600	Weak transcription	Primary T cells from cord blood	blood
48	chr3:113097800-113101000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:113097800-113105800	Weak transcription	Fetal Intestine Large	intestine
50	chr3:113097800-113117800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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