Variant report

Variant	rs62140277
Chromosome Location	chr2:53130402-53130403
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10490579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10490583	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11901541	0.85[EUR][1000 genomes]
rs17039478	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17043472	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17043496	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17043590	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17043734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17043739	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17043781	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17043797	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17043801	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17043805	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17043807	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17043809	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17571144	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2116006	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34049687	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41392646	0.81[EUR][1000 genomes]
rs4672007	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55778790	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56286124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58269079	0.81[EUR][1000 genomes]
rs62128173	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62128174	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62128201	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62128203	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62128205	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62138243	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62138246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62138247	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62138248	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62138249	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62138250	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140275	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140278	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140279	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140280	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62140281	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62140283	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140284	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140285	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62140286	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62140287	0.95[EUR][1000 genomes]
rs62140291	0.88[EUR][1000 genomes]
rs62140292	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs725865	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793423	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72793432	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72808329	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72808339	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv2763631	chr2:52910862-53169629	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006244	chr2:52958322-53169617	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
5	nsv1014068	chr2:52960353-53169617	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	esv33728	chr2:53125665-53131680	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
12	nsv1007543	chr2:53129090-53148411	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	nsv1009138	chr2:53129701-53167075	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53109400-53145600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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