Variant report

Variant	rs1978654
Chromosome Location	chr2:53161102-53161103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10175099	0.91[ASN][1000 genomes]
rs10490578	0.91[ASN][1000 genomes]
rs1077945	0.89[ASN][1000 genomes]
rs11125460	0.91[ASN][1000 genomes]
rs1154747	0.95[ASN][1000 genomes]
rs12232928	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12232931	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12232966	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12233020	0.96[ASN][1000 genomes]
rs12233053	0.94[ASN][1000 genomes]
rs12233252	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12233257	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12474068	0.87[ASN][1000 genomes]
rs1510107	0.91[ASN][1000 genomes]
rs1510108	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1510109	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1510110	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510111	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17043826	0.91[ASN][1000 genomes]
rs17043829	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17043834	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043835	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17043857	0.89[ASN][1000 genomes]
rs1828335	0.84[ASN][1000 genomes]
rs1858211	0.89[ASN][1000 genomes]
rs1858212	0.92[ASN][1000 genomes]
rs1858213	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876937	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288639	0.88[ASN][1000 genomes]
rs2356682	0.91[ASN][1000 genomes]
rs35254490	0.88[ASN][1000 genomes]
rs35905559	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36080419	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672085	0.90[ASN][1000 genomes]
rs4672093	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672094	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55992015	0.86[ASN][1000 genomes]
rs59013056	0.88[ASN][1000 genomes]
rs59981051	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140315	0.93[ASN][1000 genomes]
rs62140317	0.95[ASN][1000 genomes]
rs62140318	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140326	0.87[ASN][1000 genomes]
rs66762357	0.94[ASN][1000 genomes]
rs6723602	0.83[ASN][1000 genomes]
rs72793436	0.91[ASN][1000 genomes]
rs72793440	0.93[ASN][1000 genomes]
rs72793445	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72793448	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72793458	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7422475	0.91[ASN][1000 genomes]
rs7585428	0.91[ASN][1000 genomes]
rs7596997	0.86[ASN][1000 genomes]
rs7597431	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
12	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

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53159200-53162200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:53160200-53161400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:53160200-53161800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:53160200-53163200	Enhancers	Hela-S3	cervix
5	chr2:53160600-53162600	Enhancers	NH-A	brain
6	chr2:53160600-53162800	Enhancers	Osteobl	bone
7	chr2:53160800-53161200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:53160800-53161200	Enhancers	A549	lung
9	chr2:53160800-53161400	Enhancers	Fetal Intestine Small	intestine
10	chr2:53160800-53161600	Flanking Active TSS	HMEC	breast
11	chr2:53161000-53161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:53161000-53161200	Enhancers	Fetal Intestine Large	intestine
13	chr2:53161000-53161400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:53161000-53161800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:53161000-53161800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:53161000-53161800	Enhancers	NHLF	lung
17	chr2:53161000-53162200	Enhancers	GM12878-XiMat	blood
18	chr2:53161000-53162400	Enhancers	NHEK	skin

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