Variant report

Variant	rs2643039
Chromosome Location	chr4:62312744-62312745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1037671	0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10517536	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11131326	1.00[EUR][1000 genomes]
rs1350247	0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1379166	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1379167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456867	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456875	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456878	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1497902	1.00[EUR][1000 genomes]
rs1497904	1.00[EUR][1000 genomes]
rs1531204	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17090502	1.00[EUR][1000 genomes]
rs17090511	1.00[EUR][1000 genomes]
rs17090512	1.00[EUR][1000 genomes]
rs17090513	1.00[EUR][1000 genomes]
rs1845582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124795	0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124796	0.89[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2219342	1.00[EUR][1000 genomes]
rs2606712	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606714	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606715	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606717	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2643035	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2643037	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2643038	0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2643040	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335275	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335276	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335280	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335281	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs335283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335284	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335293	1.00[EUR][1000 genomes]
rs335297	1.00[EUR][1000 genomes]
rs335298	1.00[EUR][1000 genomes]
rs335326	1.00[EUR][1000 genomes]
rs335327	1.00[EUR][1000 genomes]
rs335328	1.00[EUR][1000 genomes]
rs335330	1.00[EUR][1000 genomes]
rs335331	1.00[EUR][1000 genomes]
rs335333	1.00[EUR][1000 genomes]
rs335339	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335343	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335344	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335345	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335346	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335347	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4860413	1.00[EUR][1000 genomes]
rs6551630	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6814707	0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823672	1.00[EUR][1000 genomes]
rs6834543	0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6841033	1.00[EUR][1000 genomes]
rs7655377	1.00[EUR][1000 genomes]
rs7660777	1.00[EUR][1000 genomes]
rs7683598	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7687816	0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7693587	1.00[EUR][1000 genomes]
rs7693679	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7698624	1.00[EUR][1000 genomes]
rs9654273	1.00[EUR][1000 genomes]
rs991586	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs991587	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs991588	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv879075	chr4:62124531-62354791	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv868844	chr4:62241702-62497248	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv879076	chr4:62251077-62354791	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2753138	chr4:62271444-62442507	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62294000-62328000	Weak transcription	Fetal Stomach	stomach
2	chr4:62309600-62314200	Enhancers	Fetal Intestine Large	intestine
3	chr4:62310200-62313800	Weak transcription	Brain Anterior Caudate	brain
4	chr4:62310400-62313600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:62310600-62313600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:62310800-62313600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:62310800-62313800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:62311000-62313600	Weak transcription	NHEK	skin
9	chr4:62311000-62314000	Weak transcription	Stomach Mucosa	stomach
10	chr4:62311600-62313600	Weak transcription	Fetal Heart	heart
11	chr4:62311800-62313600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:62312000-62317400	Weak transcription	Fetal Intestine Small	intestine
13	chr4:62312400-62313800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:62312600-62312800	Enhancers	Brain Cingulate Gyrus	brain
15	chr4:62312600-62312800	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr4:62312600-62314000	Enhancers	Brain Hippocampus Middle	brain
17	chr4:62312600-62314000	Enhancers	Brain Substantia Nigra	brain
18	chr4:62312600-62317800	Weak transcription	Small Intestine	intestine

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