Variant report

Variant	rs6048590
Chromosome Location	chr20:23182977-23182978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23122546..23124571-chr20:23180527..23183160,2	MCF-7	breast:
2	chr20:23181615..23184687-chr20:23185020..23187580,3	K562	blood:
3	chr20:23181724..23187567-chr20:23190860..23194115,6	MCF-7	breast:
4	chr20:23066160..23068194-chr20:23180754..23182978,2	K562	blood:
5	chr20:23167086..23169552-chr20:23181664..23183709,2	K562	blood:
6	chr20:23182243..23184048-chr20:23189878..23191946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125810	Chromatin interaction
ENSG00000230387	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005856	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1099456	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11696272	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1338944	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1416399	0.89[ASN][1000 genomes]
rs1538445	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1538446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1572707	0.88[ASN][1000 genomes]
rs1856470	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2024897	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6036338	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048591	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048592	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048612	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048615	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048618	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048619	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6076038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6076039	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6076041	0.96[CHB][hapmap];0.96[JPT][hapmap];0.90[ASN][1000 genomes]
rs6083030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083032	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083033	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6083036	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6083038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6083042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6083043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6106616	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6113992	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132576	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132577	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132578	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132579	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62206882	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62206883	0.83[AMR][1000 genomes]
rs750652	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8118328	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844924	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs844929	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs844930	0.97[ASN][1000 genomes]
rs844932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844935	0.83[AMR][1000 genomes]
rs844936	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844938	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844940	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844941	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867909	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs870225	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912817	chr20:23127661-23240969	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066734	chr20:23170094-23277628	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23179200-23183600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr20:23179400-23183600	Weak transcription	NHDF-Ad	bronchial
3	chr20:23180800-23184800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:23181200-23183800	Enhancers	Right Ventricle	heart
5	chr20:23181600-23183400	Weak transcription	Right Atrium	heart
6	chr20:23181800-23184400	Enhancers	Fetal Muscle Leg	muscle
7	chr20:23181800-23185000	Weak transcription	Esophagus	oesophagus
8	chr20:23182000-23185000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:23182000-23186600	Weak transcription	Lung	lung
10	chr20:23182200-23183400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr20:23182200-23185000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr20:23182200-23185000	Weak transcription	Placenta	Placenta
13	chr20:23182200-23185600	Weak transcription	Stomach Mucosa	stomach
14	chr20:23182600-23183000	Weak transcription	Colon Smooth Muscle	Colon
15	chr20:23182600-23183600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr20:23182600-23183600	Weak transcription	Adipose Nuclei	Adipose
17	chr20:23182600-23184600	Weak transcription	K562	blood
18	chr20:23182600-23185000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr20:23182600-23185000	Weak transcription	Left Ventricle	heart
20	chr20:23182600-23186200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr20:23182600-23187800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr20:23182800-23185800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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