Variant report

Variant	rs4815142
Chromosome Location	chr20:22743299-22743300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22737582..22739507-chr20:22742394..22744607,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1997880	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2424462	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424463	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424467	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424471	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424472	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424474	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424477	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424478	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048344	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082809	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082843	0.80[EUR][1000 genomes]
rs6113805	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132546	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137748	0.90[ASN][1000 genomes]
rs932466	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4815142	SLC24A3	cis	parietal	SCAN
rs4815142	GINS1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22734800-22745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:22737800-22749000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:22739600-22743400	Weak transcription	Aorta	Aorta
4	chr20:22739600-22743600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr20:22740000-22744600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr20:22740800-22746000	Enhancers	Placenta	Placenta
7	chr20:22741200-22743400	Weak transcription	Right Atrium	heart
8	chr20:22741400-22743400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr20:22741400-22743600	Enhancers	HSMMtube	muscle
10	chr20:22741600-22743400	Weak transcription	Esophagus	oesophagus
11	chr20:22741600-22745200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:22742200-22743400	Enhancers	HMEC	breast
13	chr20:22742200-22745800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr20:22742400-22743600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:22742400-22746000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:22742400-22746000	Enhancers	Lung	lung
17	chr20:22742600-22744000	Enhancers	HSMM	muscle
18	chr20:22742800-22743400	Enhancers	Hela-S3	cervix
19	chr20:22742800-22744800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr20:22742800-22745800	Enhancers	Stomach Mucosa	stomach
21	chr20:22743000-22743600	Enhancers	A549	lung
22	chr20:22743000-22743800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr20:22743000-22744600	Flanking Active TSS	NHEK	skin
24	chr20:22743000-22744800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:22743000-22745200	Weak transcription	Spleen	Spleen
26	chr20:22743200-22743600	Enhancers	Gastric	stomach
27	chr20:22743200-22743800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr20:22743200-22743800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr20:22743200-22744000	Enhancers	Left Ventricle	heart
30	chr20:22743200-22744400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr20:22743200-22745400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr20:22743200-22745400	Enhancers	Fetal Heart	heart
33	chr20:22743200-22745800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:22743200-22745800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:22743200-22746600	Enhancers	Fetal Muscle Leg	muscle
36	chr20:22743200-22751400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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