Variant report

Variant	rs6425046
Chromosome Location	chr1:186744362-186744363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLA2G4A-8	chr1:186744292-186744419	NONHSAT008452

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10489400	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10737268	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10752972	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10752975	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10798058	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12022878	0.86[AFR][1000 genomes]
rs12088741	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124257	1.00[EUR][1000 genomes]
rs12136874	0.92[EUR][1000 genomes]
rs12725481	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12738146	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1883272	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1997673	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2064131	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2064132	1.00[EUR][1000 genomes]
rs2142817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2142818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2179225	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2205952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2223328	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2383532	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2891253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2891254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3955272	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140563	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140564	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4650702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4651325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4651326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6425045	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6425047	1.00[EUR][1000 genomes]
rs66476634	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656831	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669569	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7517157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7521061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522771	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537367	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552522	1.00[EUR][1000 genomes]
rs760707	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs760708	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs760709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs988904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs988905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv466272	chr1:186742947-186803226	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv548406	chr1:186742947-186803226	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186741400-186745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:186743400-186745400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:186743400-186745600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:186743600-186744400	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:186743800-186745400	Enhancers	Fetal Lung	lung

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