Variant report

Variant	rs2086880
Chromosome Location	chr3:136751968-136751969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs108858	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13095028	0.83[CEU][hapmap]
rs13095034	0.85[EUR][1000 genomes]
rs1385306	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1470142	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1654900	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654901	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1682361	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1682362	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1682363	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1682364	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1682365	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1682366	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs181732	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2117008	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2344092	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34564994	0.85[EUR][1000 genomes]
rs361227	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs361228	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs361229	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs361231	0.85[EUR][1000 genomes]
rs361232	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs361233	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361234	0.86[EUR][1000 genomes]
rs361235	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4678278	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678281	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55781515	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6439677	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439678	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6766766	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766858	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802479	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754694	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7640951	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7646307	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835627	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs835628	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835629	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835630	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835631	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835651	0.83[EUR][1000 genomes]
rs835652	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs900947	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900948	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs900949	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs900950	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9681468	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9817061	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9827066	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9845076	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs9850024	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9854795	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9874615	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs999038	0.86[AMR][1000 genomes];0.90[EUR][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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136745800-136755000	Weak transcription	NHEK	skin
2	chr3:136748000-136754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:136750800-136752000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:136751000-136752000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:136751000-136752000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:136751000-136752000	Active TSS	Stomach Smooth Muscle	stomach
7	chr3:136751000-136752000	Active TSS	A549	lung
8	chr3:136751000-136752400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:136751200-136752000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:136751200-136752000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:136751200-136752000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:136751200-136752000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr3:136751200-136752000	Flanking Active TSS	Liver	Liver
14	chr3:136751200-136752000	Active TSS	Brain Angular Gyrus	brain
15	chr3:136751200-136752000	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr3:136751200-136752000	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr3:136751200-136752000	Active TSS	HSMM	muscle
18	chr3:136751200-136752000	Active TSS	Osteobl	bone
19	chr3:136751400-136752000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:136751400-136752000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:136751400-136752000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:136751400-136752000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:136751400-136752000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:136751400-136752000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:136751400-136752000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:136751400-136752000	Active TSS	Fetal Brain Male	brain
27	chr3:136751400-136752000	Enhancers	Fetal Heart	heart
28	chr3:136751400-136752000	Bivalent/Poised TSS	Fetal Lung	lung
29	chr3:136751400-136752000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr3:136751400-136752000	Enhancers	Spleen	Spleen
31	chr3:136751400-136752200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr3:136751600-136752000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
33	chr3:136751600-136752000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:136751600-136752000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:136751600-136752000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
36	chr3:136751600-136752000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:136751600-136752000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:136751600-136752000	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr3:136751600-136752000	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr3:136751600-136752000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr3:136751600-136752000	Enhancers	Gastric	stomach
42	chr3:136751600-136752000	Enhancers	Lung	lung
43	chr3:136751600-136752000	Enhancers	Pancreas	Pancrea
44	chr3:136751600-136752000	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr3:136751600-136752000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
46	chr3:136751600-136752000	Flanking Active TSS	HUVEC	blood vessel
47	chr3:136751600-136752200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:136751600-136752200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:136751600-136752200	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr3:136751600-136752600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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