Variant report

Variant	rs1883091
Chromosome Location	chr3:45882779-45882780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11130077	0.81[ASN][1000 genomes]
rs1129183	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318088	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488370	0.81[ASN][1000 genomes]
rs1883092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531756	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2633734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742364	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742365	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607988	0.85[AFR][1000 genomes]
rs3774643	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45558831	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683143	0.96[ASN][1000 genomes]
rs60103812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61157369	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836780	1.00[YRI][hapmap]
rs9844499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849511	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879869	1.00[YRI][hapmap]
rs9882270	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45862000-45882800	Weak transcription	Psoas Muscle	Psoas
2	chr3:45870400-45882800	Weak transcription	Gastric	stomach
3	chr3:45872400-45882800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:45872400-45883000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:45873600-45882800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:45875600-45883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:45876600-45882800	Weak transcription	Esophagus	oesophagus
8	chr3:45878400-45882800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:45882200-45882800	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr3:45882200-45883000	Flanking Active TSS	Liver	Liver
11	chr3:45882200-45884000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:45882200-45884000	Active TSS	Thymus	Thymus
13	chr3:45882200-45884200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:45882200-45886600	Strong transcription	Dnd41	blood
15	chr3:45882400-45882800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:45882400-45882800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:45882400-45882800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:45882400-45882800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:45882400-45882800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:45882400-45882800	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr3:45882400-45882800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:45882400-45882800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:45882400-45882800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:45882400-45882800	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr3:45882400-45882800	Flanking Active TSS	HMEC	breast
26	chr3:45882400-45883000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:45882400-45883000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:45882400-45883000	Flanking Active TSS	Fetal Thymus	thymus
29	chr3:45882400-45883000	Enhancers	Small Intestine	intestine
30	chr3:45882400-45883000	Flanking Active TSS	NHEK	skin
31	chr3:45882400-45883200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:45882400-45883200	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr3:45882400-45883200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:45882400-45883200	Flanking Active TSS	Fetal Brain Male	brain
35	chr3:45882400-45883200	Flanking Active TSS	Fetal Brain Female	brain
36	chr3:45882400-45883800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:45882400-45884000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:45882400-45884000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:45882400-45884200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr3:45882400-45884400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:45882600-45882800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr3:45882600-45882800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr3:45882600-45882800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
44	chr3:45882600-45882800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:45882600-45882800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:45882600-45882800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:45882600-45882800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:45882600-45882800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:45882600-45882800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr3:45882600-45882800	Enhancers	Primary monocytes fromperipheralblood	blood

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