Variant report

Variant	rs2404492
Chromosome Location	chr20:22775615-22775616
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	chr20:22770829..22772880-chr20:22773883..22775760,2	MCF-7	breast:
4	chr20:22774202..22776469-chr20:22777682..22779522,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10735149	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11087397	0.91[ASN][1000 genomes]
rs11697574	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11699126	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11699192	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11906177	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11906209	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11906222	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11906944	0.89[ASN][1000 genomes]
rs13042234	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13043348	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16984461	0.89[ASN][1000 genomes]
rs17681000	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17681083	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2103766	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2143903	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179857	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179858	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34023416	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35049078	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35465115	0.89[EUR][1000 genomes]
rs4414746	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55650525	0.89[ASN][1000 genomes]
rs6075949	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6075950	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075951	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075953	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075954	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6075955	0.89[ASN][1000 genomes]
rs6075956	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075962	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075963	0.84[ASN][1000 genomes]
rs6075964	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075965	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075966	0.89[ASN][1000 genomes]
rs6082813	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082815	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082816	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082817	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082818	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082819	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082822	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082825	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6082827	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082828	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082829	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082830	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082832	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082833	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082836	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082837	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082838	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082839	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082840	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082841	0.91[ASN][1000 genomes]
rs6082842	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7274509	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7274843	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7353078	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73900571	0.85[ASN][1000 genomes]
rs8116991	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8119685	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8122403	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8122474	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8123509	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs926744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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
rs2404492	RALGAPA2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22770600-22775800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:22771000-22776000	Weak transcription	Ovary	ovary
3	chr20:22772000-22778600	Enhancers	HMEC	breast
4	chr20:22772200-22777400	Enhancers	Placenta	Placenta
5	chr20:22773800-22776000	Weak transcription	Right Atrium	heart
6	chr20:22774000-22776600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:22774000-22778200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr20:22774200-22776000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:22774200-22778600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:22774200-22778600	Enhancers	Fetal Muscle Leg	muscle
11	chr20:22774200-22778600	Enhancers	HUVEC	blood vessel
12	chr20:22774400-22778400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:22774600-22776200	Enhancers	HSMMtube	muscle
14	chr20:22774600-22776800	Enhancers	Stomach Mucosa	stomach
15	chr20:22774600-22777600	Enhancers	Hela-S3	cervix
16	chr20:22774800-22776200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:22774800-22776200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr20:22774800-22776400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr20:22774800-22776600	Enhancers	Aorta	Aorta
20	chr20:22774800-22777400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr20:22774800-22777400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr20:22774800-22777800	Enhancers	Fetal Stomach	stomach
23	chr20:22774800-22778800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:22774800-22779000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:22774800-22779000	Enhancers	NHEK	skin
26	chr20:22775000-22776000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr20:22775000-22776000	Weak transcription	NHLF	lung
28	chr20:22775000-22776400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr20:22775000-22776600	Enhancers	Gastric	stomach
30	chr20:22775000-22778000	Enhancers	NHDF-Ad	bronchial
31	chr20:22775000-22778200	Enhancers	HSMM	muscle
32	chr20:22775200-22777600	Enhancers	Adipose Nuclei	Adipose
33	chr20:22775200-22778200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr20:22775400-22775800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr20:22775400-22776000	Enhancers	NH-A	brain
36	chr20:22775400-22776400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:22775400-22776400	Enhancers	Esophagus	oesophagus
38	chr20:22775400-22776400	Enhancers	Fetal Muscle Trunk	muscle
39	chr20:22775400-22776600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:22775400-22776600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:22775400-22776600	Enhancers	Lung	lung
42	chr20:22775400-22777800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:22775400-22778600	Enhancers	Spleen	Spleen
44	chr20:22775600-22777400	Flanking Active TSS	A549	lung

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