Variant report

Variant	rs2288639
Chromosome Location	chr2:53188267-53188268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10175099	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10490578	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1073802	0.85[EUR][1000 genomes]
rs1077945	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125460	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125468	0.86[EUR][1000 genomes]
rs1154747	0.86[ASN][1000 genomes]
rs11681279	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12232928	0.89[ASN][1000 genomes]
rs12232931	0.89[ASN][1000 genomes]
rs12232966	0.91[ASN][1000 genomes]
rs12233020	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12233053	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12233252	0.90[ASN][1000 genomes]
rs12474068	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12476447	0.80[EUR][1000 genomes]
rs1374255	0.90[EUR][1000 genomes]
rs1376571	0.82[EUR][1000 genomes]
rs1510107	0.81[ASN][1000 genomes]
rs1510108	0.89[ASN][1000 genomes]
rs1510109	0.89[ASN][1000 genomes]
rs1510110	0.88[ASN][1000 genomes]
rs1510111	0.89[ASN][1000 genomes]
rs17043826	0.86[ASN][1000 genomes]
rs17043829	0.91[ASN][1000 genomes]
rs17043834	0.90[ASN][1000 genomes]
rs17043835	0.91[ASN][1000 genomes]
rs17043857	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17044006	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17044037	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1828335	0.93[ASN][1000 genomes]
rs1858211	0.82[ASN][1000 genomes]
rs1858212	0.82[ASN][1000 genomes]
rs1858213	0.89[ASN][1000 genomes]
rs1876937	0.90[ASN][1000 genomes]
rs1912390	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1978654	0.88[ASN][1000 genomes]
rs2195660	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2356682	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35254490	0.82[ASN][1000 genomes]
rs35905559	0.90[ASN][1000 genomes]
rs36080419	0.89[ASN][1000 genomes]
rs4672085	0.82[ASN][1000 genomes]
rs4672093	0.91[ASN][1000 genomes]
rs4672094	0.91[ASN][1000 genomes]
rs4672154	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55992015	0.86[ASN][1000 genomes]
rs59013056	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59981051	0.90[ASN][1000 genomes]
rs62138364	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62140315	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62140317	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62140318	0.92[ASN][1000 genomes]
rs62140326	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66762357	0.87[ASN][1000 genomes]
rs6723602	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72793436	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72793440	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72793445	0.89[ASN][1000 genomes]
rs72793448	0.91[ASN][1000 genomes]
rs72793458	0.94[ASN][1000 genomes]
rs72795360	0.80[EUR][1000 genomes]
rs7422475	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7585428	0.85[ASN][1000 genomes]
rs7596997	0.91[ASN][1000 genomes]
rs7597431	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998380	chr2:52891706-53222155	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1010978	chr2:52959769-53249951	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv581978	chr2:53091691-53227749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv874136	chr2:53101066-53218774	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv874137	chr2:53114775-53216917	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv874138	chr2:53114775-53218774	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv3693331	chr2:53159702-53192269	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv963875	chr2:53173006-53196302	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv1012463	chr2:53187151-53377118	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53185800-53194000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:53188200-53188600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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