Variant report

Variant	rs339679
Chromosome Location	chr3:42798243-42798244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11129971	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13062528	0.95[YRI][hapmap]
rs1564176	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339663	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35426298	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683334	0.95[YRI][hapmap]
rs5027058	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778695	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7610350	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611520	1.00[AMR][1000 genomes]
rs7612614	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.81[AFR][1000 genomes]
rs7648688	0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9755640	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	0.85[AMR][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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:42788800-42799800	Weak transcription	Left Ventricle	heart
5	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:42791600-42803000	Weak transcription	Colonic Mucosa	Colon
8	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
9	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:42792000-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:42793600-42802600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:42793600-42802600	Weak transcription	Brain Substantia Nigra	brain
13	chr3:42793600-42811000	Weak transcription	Lung	lung
14	chr3:42795600-42814000	Weak transcription	Gastric	stomach
15	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
16	chr3:42796000-42799000	Enhancers	Fetal Intestine Large	intestine
17	chr3:42796000-42799000	Enhancers	Fetal Intestine Small	intestine
18	chr3:42796400-42801400	Weak transcription	Placenta	Placenta
19	chr3:42797000-42798400	Enhancers	Adipose Nuclei	Adipose
20	chr3:42797200-42798400	Enhancers	Duodenum Mucosa	Duodenum
21	chr3:42797200-42798600	Enhancers	Liver	Liver
22	chr3:42797200-42798600	Enhancers	Stomach Mucosa	stomach
23	chr3:42797600-42799200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:42797600-42802800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:42797600-42803800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:42797800-42799600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:42797800-42800400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:42797800-42801000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:42798000-42799200	Enhancers	HepG2	liver
30	chr3:42798000-42801200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:42798200-42798800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr3:42798200-42800800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:42798200-42802600	Weak transcription	Brain Anterior Caudate	brain

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