Variant report

Variant	rs4307005
Chromosome Location	chr4:158939328-158939329
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10517684	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10517688	0.83[CHB][hapmap]
rs10857307	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10857308	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11100145	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12498860	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501025	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504989	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12505752	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12505934	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12510436	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12511544	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12511578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12511957	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512064	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12643255	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12644342	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12650454	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1375138	0.81[EUR][1000 genomes]
rs17036918	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17036921	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17037241	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs1839129	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1839130	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2245735	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2594763	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2594769	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35146306	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35354204	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3934848	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4077777	0.83[ASN][1000 genomes]
rs4129400	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4132016	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4132443	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4398571	0.85[CEU][hapmap]
rs4460050	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4464607	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4629502	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4637451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691449	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57156989	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58762368	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62335304	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335305	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335306	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335307	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335308	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335310	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335311	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335313	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335314	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335315	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335316	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335317	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335339	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62335341	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62335345	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62335346	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335358	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62335359	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62336960	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62336961	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62336984	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6536298	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6814979	0.80[JPT][hapmap]
rs6815131	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6827475	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965897	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72967808	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72967836	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7384	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap]
rs7692254	0.80[JPT][hapmap]
rs964237	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs982239	0.94[AMR][1000 genomes];0.94[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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158923800-158939400	Weak transcription	HepG2	liver
2	chr4:158930200-158940800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:158930400-158940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:158930600-158940800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:158930800-158941400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:158932600-158941400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:158934200-158941400	Enhancers	HUVEC	blood vessel
8	chr4:158934600-158943800	Enhancers	NHDF-Ad	bronchial
9	chr4:158935600-158939400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:158936000-158941600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:158936200-158939600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:158936200-158942600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:158936600-158941200	Weak transcription	NHEK	skin
14	chr4:158936800-158939400	Weak transcription	HSMMtube	muscle
15	chr4:158936800-158939600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:158936800-158940800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:158936800-158941400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:158937200-158939600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:158937200-158947000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:158937200-158947200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:158938000-158940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:158938000-158941400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:158938000-158941400	Weak transcription	Adipose Nuclei	Adipose
24	chr4:158938000-158941400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:158938200-158939400	Weak transcription	NH-A	brain
26	chr4:158938200-158940800	Weak transcription	A549	lung
27	chr4:158938200-158940800	Weak transcription	HMEC	breast
28	chr4:158938400-158939400	Weak transcription	Osteobl	bone
29	chr4:158938600-158939800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr4:158938800-158939800	Enhancers	NHLF	lung
31	chr4:158938800-158942800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:158938800-158942800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:158939000-158939800	Enhancers	Ovary	ovary
34	chr4:158939200-158939800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr4:158939200-158939800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr4:158939200-158940000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:158939200-158940200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:158939200-158942200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:158939200-158942800	Enhancers	HSMM	muscle

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