Variant report

Variant	rs2404493
Chromosome Location	chr20:22775864-22775865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:22758707..22761958-chr20:22773482..22776532,3	MCF-7	breast:
2	chr20:22751785..22755071-chr20:22774743..22777587,3	MCF-7	breast:
3	chr20:22774202..22776469-chr20:22777682..22779522,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1761	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2092660	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2143902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2179856	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2179859	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424461	0.91[EUR][1000 genomes]
rs2424464	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2424465	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2424466	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2424468	0.95[EUR][1000 genomes]
rs2424469	0.95[EUR][1000 genomes]
rs2424470	0.95[EUR][1000 genomes]
rs2424473	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424475	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424476	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516506	0.95[EUR][1000 genomes]
rs4815144	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075947	0.93[EUR][1000 genomes]
rs6075948	0.95[EUR][1000 genomes]
rs6082814	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6113803	0.95[EUR][1000 genomes]
rs6113810	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
2	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv3334	chr20:22773462-22818362	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2404493	GINS1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22771000-22776000	Weak transcription	Ovary	ovary
2	chr20:22772000-22778600	Enhancers	HMEC	breast
3	chr20:22772200-22777400	Enhancers	Placenta	Placenta
4	chr20:22773800-22776000	Weak transcription	Right Atrium	heart
5	chr20:22774000-22776600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:22774000-22778200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr20:22774200-22776000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:22774200-22778600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:22774200-22778600	Enhancers	Fetal Muscle Leg	muscle
10	chr20:22774200-22778600	Enhancers	HUVEC	blood vessel
11	chr20:22774400-22778400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:22774600-22776200	Enhancers	HSMMtube	muscle
13	chr20:22774600-22776800	Enhancers	Stomach Mucosa	stomach
14	chr20:22774600-22777600	Enhancers	Hela-S3	cervix
15	chr20:22774800-22776200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:22774800-22776200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr20:22774800-22776400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:22774800-22776600	Enhancers	Aorta	Aorta
19	chr20:22774800-22777400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr20:22774800-22777400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:22774800-22777800	Enhancers	Fetal Stomach	stomach
22	chr20:22774800-22778800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:22774800-22779000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:22774800-22779000	Enhancers	NHEK	skin
25	chr20:22775000-22776000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr20:22775000-22776000	Weak transcription	NHLF	lung
27	chr20:22775000-22776400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr20:22775000-22776600	Enhancers	Gastric	stomach
29	chr20:22775000-22778000	Enhancers	NHDF-Ad	bronchial
30	chr20:22775000-22778200	Enhancers	HSMM	muscle
31	chr20:22775200-22777600	Enhancers	Adipose Nuclei	Adipose
32	chr20:22775200-22778200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr20:22775400-22776000	Enhancers	NH-A	brain
34	chr20:22775400-22776400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr20:22775400-22776400	Enhancers	Esophagus	oesophagus
36	chr20:22775400-22776400	Enhancers	Fetal Muscle Trunk	muscle
37	chr20:22775400-22776600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr20:22775400-22776600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:22775400-22776600	Enhancers	Lung	lung
40	chr20:22775400-22777800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr20:22775400-22778600	Enhancers	Spleen	Spleen
42	chr20:22775600-22777400	Flanking Active TSS	A549	lung
43	chr20:22775800-22776600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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