Variant report

Variant	rs1424972
Chromosome Location	chr2:53356999-53357000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13383171	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13414722	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1424971	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189196	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17267769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6738307	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741659	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596810	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309237	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1011118	chr2:53328397-53375220	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1424972	ERLEC1	cis	cerebellum	SCAN
rs1424972	CHAC2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53338400-53362600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:53354600-53360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:53356000-53357200	Enhancers	Brain Germinal Matrix	brain
4	chr2:53356000-53358800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:53356600-53357000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:53356600-53358200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:53356600-53359000	Enhancers	Osteobl	bone
8	chr2:53356600-53359200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:53356600-53359200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:53356600-53359200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:53356600-53359200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:53356600-53359200	Enhancers	Hela-S3	cervix
13	chr2:53356600-53359200	Enhancers	HSMM	muscle
14	chr2:53356600-53359200	Enhancers	HSMMtube	muscle
15	chr2:53356600-53359400	Enhancers	HMEC	breast
16	chr2:53356600-53359400	Enhancers	NHEK	skin
17	chr2:53356800-53357000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:53356800-53357400	Enhancers	Adipose Nuclei	Adipose
19	chr2:53356800-53357600	Enhancers	NHLF	lung
20	chr2:53356800-53357800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:53356800-53357800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:53356800-53357800	Enhancers	NH-A	brain
23	chr2:53356800-53359200	Enhancers	NHDF-Ad	bronchial
24	chr2:53356800-53359400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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