Variant report

Variant	rs56368885
Chromosome Location	chr6:56643532-56643533
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:124)

rs_ID	r²[population]
rs10498812	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10498813	0.86[EUR][1000 genomes]
rs11756551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11970648	0.87[EUR][1000 genomes]
rs13190854	0.85[EUR][1000 genomes]
rs13192540	0.82[EUR][1000 genomes]
rs13192931	0.82[EUR][1000 genomes]
rs13194625	0.86[EUR][1000 genomes]
rs13194904	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13198204	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13198399	0.89[AMR][1000 genomes]
rs13198938	0.81[AMR][1000 genomes]
rs13200166	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13200559	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13200868	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13201639	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13201733	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13203000	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13203681	0.82[EUR][1000 genomes]
rs13204466	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13205667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13207768	0.81[EUR][1000 genomes]
rs13208409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13217390	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13218913	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13219942	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13220618	0.86[EUR][1000 genomes]
rs13220628	0.86[EUR][1000 genomes]
rs13220851	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.81[EUR][1000 genomes]
rs16888171	0.90[EUR][1000 genomes]
rs17684730	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684772	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684784	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684802	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684878	0.82[EUR][1000 genomes]
rs17684884	0.82[EUR][1000 genomes]
rs17751966	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751977	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17752002	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17752046	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17752106	0.82[EUR][1000 genomes]
rs34171958	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34228698	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34359353	0.89[EUR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34455199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34465210	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34500949	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34520435	0.89[EUR][1000 genomes]
rs34566275	0.95[AMR][1000 genomes]
rs34587484	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34614087	0.85[EUR][1000 genomes]
rs34623351	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34640766	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34803237	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34832779	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34896026	0.85[EUR][1000 genomes]
rs34966024	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35073881	0.82[EUR][1000 genomes]
rs35080938	0.82[EUR][1000 genomes]
rs35081015	0.86[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs35242294	0.81[EUR][1000 genomes]
rs35251663	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35326806	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35440822	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35461301	0.85[EUR][1000 genomes]
rs35494794	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35566812	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35609883	0.90[EUR][1000 genomes]
rs35642890	0.90[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35851452	0.85[EUR][1000 genomes]
rs35873865	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35876418	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35886823	0.88[EUR][1000 genomes]
rs35986172	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36022925	0.88[EUR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36094082	0.82[EUR][1000 genomes]
rs41267675	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4299824	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4348308	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4371846	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4415160	0.85[EUR][1000 genomes]
rs4457154	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4532444	0.86[EUR][1000 genomes]
rs4587171	0.87[EUR][1000 genomes]
rs58980183	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59432342	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61601344	0.93[EUR][1000 genomes]
rs62411366	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62411367	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62411375	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62411376	0.93[EUR][1000 genomes]
rs6904535	0.98[EUR][1000 genomes]
rs6905603	0.81[EUR][1000 genomes]
rs6914293	0.81[EUR][1000 genomes]
rs6918949	0.81[EUR][1000 genomes]
rs6928104	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6934714	0.84[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71564855	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71564856	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71564861	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71564863	0.82[EUR][1000 genomes]
rs7758867	0.85[EUR][1000 genomes]
rs7761501	0.82[EUR][1000 genomes]
rs7761729	0.81[EUR][1000 genomes]
rs7771085	0.88[EUR][1000 genomes]
rs7775182	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56625600-56649800	Weak transcription	Brain Germinal Matrix	brain
2	chr6:56637800-56647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:56638000-56650200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:56638000-56653000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:56638000-56654200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:56638000-56654400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:56638000-56654800	Weak transcription	Psoas Muscle	Psoas
8	chr6:56638000-56659200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:56638000-56659200	Weak transcription	NHLF	lung
10	chr6:56638200-56651200	Weak transcription	HSMMtube	muscle
11	chr6:56638400-56647800	Weak transcription	NH-A	brain
12	chr6:56638400-56655000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:56639400-56650000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:56641200-56654800	Weak transcription	HUVEC	blood vessel
15	chr6:56641200-56659000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:56642400-56654800	Weak transcription	Brain Angular Gyrus	brain
17	chr6:56642600-56650600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:56642600-56650600	Weak transcription	HSMM	muscle
19	chr6:56642600-56651000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:56642600-56654000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:56642600-56654600	Weak transcription	A549	lung
22	chr6:56642600-56659400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:56642800-56658800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:56643000-56654600	Weak transcription	Brain Hippocampus Middle	brain

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