Variant report

Variant	rs1438541
Chromosome Location	chr3:105158278-105158279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10049426	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1036582	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10511243	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10933816	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10933817	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488994	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491980	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494392	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12695118	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13062366	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13064396	0.94[ASN][1000 genomes]
rs13092811	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13093663	0.95[AFR][1000 genomes]
rs13097669	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13100098	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1438538	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1530069	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1898654	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2164956	0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2178407	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2196745	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2399045	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28670976	0.94[ASN][1000 genomes]
rs2895299	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4426702	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4894831	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57834585	0.94[ASN][1000 genomes]
rs6437587	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6437589	0.87[ASN][1000 genomes]
rs66805489	0.87[AFR][1000 genomes]
rs6767277	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767814	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6769302	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6779807	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6780238	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796658	0.88[ASN][1000 genomes]
rs6806304	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431531	0.94[ASN][1000 genomes]
rs7615005	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629589	0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7644273	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7647011	0.94[ASN][1000 genomes]
rs7649033	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288802	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9288805	0.95[AFR][1000 genomes]
rs934856	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs975574	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9842028	0.94[ASN][1000 genomes]
rs9851952	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9883620	0.95[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9883799	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised 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 target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105137400-105178600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
3	chr3:105146400-105159200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:105146400-105162600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:105148400-105162600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:105148600-105162200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:105150400-105163400	Weak transcription	A549	lung
8	chr3:105150600-105159200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:105150800-105177800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:105152200-105166200	Weak transcription	Ovary	ovary
11	chr3:105152600-105158600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:105152800-105158800	Weak transcription	Brain Anterior Caudate	brain
13	chr3:105155800-105158600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:105155800-105177600	Weak transcription	HSMM	muscle
15	chr3:105156000-105158800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:105156000-105163000	Weak transcription	NHLF	lung
17	chr3:105157000-105159000	Weak transcription	Liver	Liver
18	chr3:105157400-105158800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:105157600-105158400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:105157600-105159400	Enhancers	Brain Hippocampus Middle	brain
21	chr3:105157600-105159800	Enhancers	Brain Substantia Nigra	brain
22	chr3:105157800-105159800	Enhancers	HepG2	liver
23	chr3:105157800-105160400	Enhancers	Fetal Heart	heart
24	chr3:105158000-105163200	Weak transcription	NHDF-Ad	bronchial
25	chr3:105158000-105163400	Weak transcription	Osteobl	bone
26	chr3:105158200-105160800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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