Variant report

Variant	rs1259339
Chromosome Location	chr3:120167006-120167007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10511400	0.85[CEU][hapmap]
rs1123897	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1123898	0.90[ASN][1000 genomes]
rs1147709	0.83[CHB][hapmap]
rs1147717	0.90[ASN][1000 genomes]
rs1147720	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs12495760	0.85[CEU][hapmap]
rs1259311	0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1259318	0.82[CHB][hapmap]
rs1259329	0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1259330	0.83[AMR][1000 genomes]
rs1259331	0.88[CHB][hapmap]
rs1259332	0.88[CHB][hapmap]
rs1259333	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs1259334	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1259335	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1259336	0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1259337	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1259338	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1259457	0.90[ASN][1000 genomes]
rs1267675	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1270209	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs1520881	0.88[CHB][hapmap]
rs1624195	0.87[MEX][hapmap];0.80[YRI][hapmap]
rs1627473	0.82[MKK][hapmap]
rs1628541	0.86[YRI][hapmap]
rs16831033	0.85[CEU][hapmap]
rs16831036	0.85[CEU][hapmap]
rs1716835	0.94[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1733296	0.82[CHB][hapmap]
rs1733299	0.85[ASN][1000 genomes]
rs1733304	0.88[CHB][hapmap]
rs1733306	0.88[CHB][hapmap]
rs1733319	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1982186	0.90[ASN][1000 genomes]
rs2252084	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2272516	0.85[CEU][hapmap]
rs2700263	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702155	0.83[CHB][hapmap]
rs6803428	0.85[CEU][hapmap]
rs874477	0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs874479	0.88[CHB][hapmap]
rs874480	0.90[ASN][1000 genomes]
rs9631455	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:120138200-120169200	Weak transcription	Gastric	stomach
3	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
4	chr3:120153000-120167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:120155800-120168400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:120156600-120168800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:120158000-120167600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:120158200-120167400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:120158800-120167400	Weak transcription	A549	lung
10	chr3:120160000-120167400	Weak transcription	HMEC	breast
11	chr3:120160000-120167600	Weak transcription	NHEK	skin
12	chr3:120160600-120167400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:120160800-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:120160800-120167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:120161000-120167400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:120161200-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:120162200-120168800	Weak transcription	Esophagus	oesophagus
18	chr3:120163000-120169000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:120163800-120167800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:120164600-120167400	Genic enhancers	Fetal Muscle Leg	muscle
21	chr3:120164600-120167400	Genic enhancers	Fetal Stomach	stomach
22	chr3:120164800-120167800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:120165000-120168400	Transcr. at gene 5' and 3'	Osteobl	bone
24	chr3:120165600-120167400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:120165600-120167600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:120165800-120167400	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr3:120165800-120167600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:120166000-120167400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:120166000-120167400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:120166000-120167400	Enhancers	Fetal Heart	heart
31	chr3:120166000-120167400	Weak transcription	Fetal Kidney	kidney
32	chr3:120166000-120167400	Weak transcription	Psoas Muscle	Psoas
33	chr3:120166000-120167400	Genic enhancers	HSMM	muscle
34	chr3:120166000-120167600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:120166000-120168000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:120166200-120167400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:120166200-120167600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:120166200-120168600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:120166400-120167200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:120166400-120167200	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr3:120166400-120167400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:120166400-120167400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:120166400-120167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:120166400-120167400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:120166400-120167400	Weak transcription	Fetal Brain Male	brain
46	chr3:120166400-120167400	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:120166400-120167400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:120166400-120167600	Weak transcription	Brain Angular Gyrus	brain
49	chr3:120166400-120167600	Weak transcription	Lung	lung
50	chr3:120166400-120168000	Enhancers	Ovary	ovary

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