Variant report

Variant	rs6556824
Chromosome Location	chr5:92856766-92856767
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11135388	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11951859	0.90[EUR][1000 genomes]
rs11952115	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11952600	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11960608	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12186735	0.93[ASN][1000 genomes]
rs12187239	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188716	0.93[ASN][1000 genomes]
rs12188845	0.92[EUR][1000 genomes]
rs12188905	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370977	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457101	0.93[EUR][1000 genomes]
rs17082127	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082129	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17083145	0.90[EUR][1000 genomes]
rs17083155	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17083181	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17083191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083198	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083213	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083228	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370695	0.93[ASN][1000 genomes]
rs1824153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1844343	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083227	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279473	0.93[ASN][1000 genomes]
rs2344387	0.92[EUR][1000 genomes]
rs3776601	0.93[ASN][1000 genomes]
rs55861967	0.90[EUR][1000 genomes]
rs57165666	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57690257	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59360932	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61324921	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61352323	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556823	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556826	0.82[EUR][1000 genomes]
rs6860632	0.88[AMR][1000 genomes]
rs6866771	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879816	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880843	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6889857	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133214	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133217	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133226	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133228	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73133239	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73133251	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133254	0.90[EUR][1000 genomes]
rs73133258	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73133261	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133265	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133275	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133278	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133280	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133283	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133287	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133289	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133292	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133301	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135313	0.88[EUR][1000 genomes]
rs73135320	0.93[ASN][1000 genomes]
rs73135321	0.93[ASN][1000 genomes]
rs73772907	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7712899	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715034	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7727107	0.93[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	nsv1022355	chr5:92846496-92911797	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
2	nsv537807	chr5:92846496-92911797	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
3	nsv882382	chr5:92853645-92891029	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92815200-92859200	Weak transcription	Fetal Brain Male	brain
2	chr5:92827000-92858200	Weak transcription	Ovary	ovary
3	chr5:92827200-92858200	Weak transcription	Fetal Stomach	stomach
4	chr5:92839600-92857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:92841400-92857400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:92841600-92858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:92847200-92857200	Weak transcription	Fetal Lung	lung
8	chr5:92850200-92857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:92854200-92857200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:92854600-92857200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:92854600-92857400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:92855400-92856800	Enhancers	HUVEC	blood vessel
13	chr5:92855400-92858000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:92855400-92858600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:92855800-92858000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:92856000-92858800	Weak transcription	HSMM	muscle
17	chr5:92856000-92859000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:92856200-92867000	Weak transcription	NHLF	lung
19	chr5:92856200-92867400	Weak transcription	Osteobl	bone
20	chr5:92856200-92868200	Weak transcription	NH-A	brain
21	chr5:92856400-92856800	Genic enhancers	Muscle Satellite Cultured Cells	--
22	chr5:92856400-92857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:92856600-92857600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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