Variant report

Variant	rs7638459
Chromosome Location	chr3:142490151-142490152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1132030	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11717993	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1382688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604	0.92[ASN][1000 genomes]
rs1871349	0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2033912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049328	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2177398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354856	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28524951	0.84[EUR][1000 genomes]
rs28658009	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661660	0.91[EUR][1000 genomes]
rs28689551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34076811	0.91[EUR][1000 genomes]
rs34445140	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3821647	0.87[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs3844273	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs4259003	0.87[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4530572	0.87[EUR][1000 genomes]
rs4539980	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs45497994	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4643748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55722370	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55722917	0.90[ASN][1000 genomes]
rs56666685	0.99[EUR][1000 genomes]
rs57026466	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59108985	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60294656	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60319320	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60752859	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440107	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs6440108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440110	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66897945	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67100994	0.81[AMR][1000 genomes]
rs6772222	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777466	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6784998	0.89[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.91[ASN][1000 genomes]
rs6790959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6791501	0.91[EUR][1000 genomes]
rs6798849	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6803681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807862	0.90[EUR][1000 genomes]
rs73232711	0.99[EUR][1000 genomes]
rs7621642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622662	0.84[EUR][1000 genomes]
rs7623762	0.82[ASW][hapmap]
rs7623977	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7626908	0.91[ASN][1000 genomes]
rs7628728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs7631245	0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7635768	0.91[EUR][1000 genomes]
rs7637826	0.91[EUR][1000 genomes]
rs7637846	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7639403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641514	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7642332	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7644704	0.92[ASN][1000 genomes]
rs7646197	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7647291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs7653309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772	0.84[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs936339	0.83[EUR][1000 genomes]
rs953641	1.00[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs9754885	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9758429	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9784320	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9815607	1.00[CEU][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820721	0.91[ASN][1000 genomes]
rs9823836	0.85[ASN][1000 genomes]
rs9824476	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9836269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841007	0.81[EUR][1000 genomes]
rs9846406	0.81[EUR][1000 genomes]
rs9849461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850734	0.84[EUR][1000 genomes]
rs9851381	0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9861598	0.86[ASN][1000 genomes]
rs9864230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865053	0.86[ASN][1000 genomes]
rs9868886	1.00[CEU][hapmap];0.99[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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142464800-142493200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:142467800-142503400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:142468200-142511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:142468200-142525200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:142468400-142498000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:142468400-142501400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:142468400-142501400	Weak transcription	HSMM	muscle
8	chr3:142468400-142501600	Weak transcription	Left Ventricle	heart
9	chr3:142468400-142508800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:142468400-142525200	Weak transcription	Fetal Brain Male	brain
11	chr3:142468400-142526800	Weak transcription	NHDF-Ad	bronchial
12	chr3:142468400-142529400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:142468600-142525200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:142468800-142492000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:142468800-142513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:142469200-142491200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:142470600-142505800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:142472400-142509800	Weak transcription	HepG2	liver
19	chr3:142475000-142527200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:142475200-142498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:142481600-142501400	Weak transcription	Fetal Stomach	stomach
22	chr3:142484600-142506400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:142487000-142502400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:142487400-142501400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:142487400-142501400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:142487400-142513600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:142487600-142503400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:142487800-142506800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:142488800-142491800	Weak transcription	Fetal Lung	lung
30	chr3:142488800-142498200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:142488800-142505000	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:142488800-142527000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:142489200-142501400	Weak transcription	Aorta	Aorta
34	chr3:142489800-142490400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:142489800-142490400	Strong transcription	Ovary	ovary
36	chr3:142489800-142490600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:142489800-142501200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:142490000-142491000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:142490000-142497200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:142490000-142503600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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