Variant report

Variant	rs28579300
Chromosome Location	chr22:28578089-28578090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10154425	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212007	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10212036	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212040	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10212074	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10212083	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10483142	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10483143	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12166023	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166077	0.82[EUR][1000 genomes]
rs12166158	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166253	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12166256	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12166719	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12166740	0.84[EUR][1000 genomes]
rs12166912	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166938	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12167735	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168054	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168180	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12168251	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12168652	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168708	0.81[AMR][1000 genomes]
rs12168851	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12169888	0.82[EUR][1000 genomes]
rs12170022	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170558	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12170953	0.82[EUR][1000 genomes]
rs134194	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs134197	1.00[ASN][1000 genomes]
rs138642	0.83[AMR][1000 genomes]
rs138651	0.82[EUR][1000 genomes]
rs138654	0.82[EUR][1000 genomes]
rs138655	0.82[EUR][1000 genomes]
rs138656	0.82[EUR][1000 genomes]
rs138658	0.82[EUR][1000 genomes]
rs138660	0.82[EUR][1000 genomes]
rs138664	0.82[EUR][1000 genomes]
rs138665	0.82[EUR][1000 genomes]
rs138667	0.82[EUR][1000 genomes]
rs138671	0.82[EUR][1000 genomes]
rs138672	0.82[EUR][1000 genomes]
rs16985967	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16985976	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986037	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16986077	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987005	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407024	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483887	0.82[EUR][1000 genomes]
rs17484337	0.82[EUR][1000 genomes]
rs2745562	0.81[EUR][1000 genomes]
rs28375646	0.82[EUR][1000 genomes]
rs4036493	0.80[EUR][1000 genomes]
rs470102	0.82[EUR][1000 genomes]
rs470103	0.82[EUR][1000 genomes]
rs470104	0.82[EUR][1000 genomes]
rs55846737	0.81[AMR][1000 genomes]
rs55856549	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56233401	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393679	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57686964	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58050941	0.80[EUR][1000 genomes]
rs58823697	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286519	0.82[EUR][1000 genomes]
rs73880374	0.82[EUR][1000 genomes]
rs73880375	0.82[EUR][1000 genomes]
rs73880376	0.82[EUR][1000 genomes]
rs73880381	0.82[EUR][1000 genomes]
rs73880383	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73880384	0.82[EUR][1000 genomes]
rs73880385	0.84[EUR][1000 genomes]
rs73880387	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73880391	1.00[ASN][1000 genomes]
rs73880393	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880395	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73882704	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73882705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73882709	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761322	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761323	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306451	0.84[EUR][1000 genomes]
rs9306452	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620762	0.82[EUR][1000 genomes]
rs9620764	0.82[EUR][1000 genomes]
rs9620766	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9620767	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9620768	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9620769	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620770	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620771	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620778	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9620779	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625387	0.82[EUR][1000 genomes]
rs9625388	0.82[EUR][1000 genomes]
rs9625390	0.82[EUR][1000 genomes]
rs9625391	0.81[EUR][1000 genomes]
rs9625393	0.82[EUR][1000 genomes]
rs9625394	1.00[ASN][1000 genomes]
rs9625395	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625396	0.84[EUR][1000 genomes]
rs9625397	0.84[EUR][1000 genomes]
rs9625398	0.84[EUR][1000 genomes]
rs9625399	0.84[EUR][1000 genomes]
rs9625400	0.84[EUR][1000 genomes]
rs9625402	0.84[EUR][1000 genomes]
rs9625403	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625405	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625406	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625407	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625408	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625409	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625410	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625413	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625415	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625416	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625417	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625418	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625421	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625430	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9625433	1.00[ASN][1000 genomes]
rs9625437	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625441	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9712839	0.86[EUR][1000 genomes]
rs988893	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28568200-28579000	Weak transcription	Left Ventricle	heart
2	chr22:28569400-28579200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr22:28570000-28581000	Weak transcription	Fetal Intestine Small	intestine
4	chr22:28572200-28597800	Weak transcription	Dnd41	blood
5	chr22:28575600-28579200	Weak transcription	Pancreas	Pancrea
6	chr22:28576600-28578800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr22:28576600-28579600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr22:28576800-28578400	Enhancers	Brain Anterior Caudate	brain
9	chr22:28576800-28578400	Enhancers	Rectal Smooth Muscle	rectum
10	chr22:28576800-28578400	Enhancers	Osteobl	bone
11	chr22:28577000-28603600	Weak transcription	Aorta	Aorta
12	chr22:28577200-28578600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr22:28577200-28579400	Enhancers	Colon Smooth Muscle	Colon
14	chr22:28577400-28578400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr22:28577400-28579200	Weak transcription	Brain Germinal Matrix	brain
16	chr22:28577400-28579400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr22:28577400-28580200	Enhancers	Adipose Nuclei	Adipose
18	chr22:28577400-28584600	Weak transcription	Fetal Brain Female	brain
19	chr22:28577600-28578400	Enhancers	Fetal Muscle Leg	muscle
20	chr22:28577600-28578400	Enhancers	Ovary	ovary
21	chr22:28577600-28579600	Enhancers	Small Intestine	intestine
22	chr22:28577800-28578200	Enhancers	Fetal Heart	heart
23	chr22:28577800-28579200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr22:28577800-28600400	Weak transcription	Right Atrium	heart
25	chr22:28578000-28578800	Weak transcription	Fetal Lung	lung
26	chr22:28578000-28579200	Weak transcription	Psoas Muscle	Psoas
27	chr22:28578000-28583200	Weak transcription	Fetal Brain Male	brain

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