Variant report

Variant	rs12649397
Chromosome Location	chr4:55019823-55019824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10011984	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10030288	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10030381	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10033457	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11133307	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1158401	0.80[AMR][1000 genomes]
rs1158402	0.80[AMR][1000 genomes]
rs11737133	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504400	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1425672	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1834432	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2033054	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2162137	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35539097	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4099487	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4864499	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554152	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6554154	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554155	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7654284	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660472	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9990683	0.92[AMR][1000 genomes];0.92[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	nsv879018	chr4:54714753-55030375	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv594203	chr4:54960005-55030375	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv879020	chr4:54986912-55064573	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv523058	chr4:55018617-55045716	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55018400-55020200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:55018400-55020400	Enhancers	HMEC	breast
3	chr4:55018400-55020400	Enhancers	NHEK	skin
4	chr4:55018600-55020000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:55018600-55020000	Enhancers	HSMMtube	muscle
6	chr4:55018600-55020200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:55018600-55020200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:55018600-55020200	Enhancers	HSMM	muscle
9	chr4:55018600-55020400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:55018800-55036200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:55019200-55022000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:55019600-55021400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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