Variant report

Variant	rs406389
Chromosome Location	chr20:52845829-52845830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52845491..52846135-chr20:53263111..53263838,3	MCF-7	breast:
2	chr20:52836129..52837011-chr20:52845467..52846140,2	MCF-7	breast:
3	chr20:52844972..52848737-chr20:53072489..53075619,3	MCF-7	breast:
4	chr1:121484850..121486543-chr20:52844002..52846741,2	MCF-7	breast:
5	chr20:52843581..52850062-chr20:52850195..52855343,9	MCF-7	breast:
6	chr20:52838765..52840477-chr20:52844593..52846830,2	K562	blood:
7	chr20:52844235..52847493-chr20:52876743..52879429,3	MCF-7	breast:
8	chr20:52838977..52840544-chr20:52845330..52847377,2	K562	blood:

No data

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs16999413	1.00[CEU][hapmap]
rs2756032	0.96[AFR][1000 genomes]
rs366424	0.96[AFR][1000 genomes]
rs367149	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs368604	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs371012	0.96[AFR][1000 genomes]
rs372987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs374623	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs377448	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs378666	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs378668	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs380980	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs383890	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs389806	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs393866	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs396957	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs404705	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs414058	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs415230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs416263	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs416724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs418191	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs422615	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs422818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs423338	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs424195	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs425792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs429350	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs432270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437970	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs446835	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6013929	1.00[EUR][1000 genomes]
rs6013931	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6013932	1.00[EUR][1000 genomes]
rs6013934	1.00[EUR][1000 genomes]
rs6023039	1.00[EUR][1000 genomes]
rs6023040	1.00[EUR][1000 genomes]
rs6023041	1.00[EUR][1000 genomes]
rs6023046	1.00[EUR][1000 genomes]
rs6023047	1.00[EUR][1000 genomes]
rs6127144	1.00[EUR][1000 genomes]
rs73285988	1.00[EUR][1000 genomes]
rs793045	1.00[CEU][hapmap]

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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
2	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:52835600-52846000	Weak transcription	HSMMtube	muscle
4	chr20:52838600-52846000	Weak transcription	Fetal Muscle Leg	muscle
5	chr20:52840600-52849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:52840800-52849000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:52841000-52851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:52845200-52846000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52845200-52846200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr20:52845400-52846200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr20:52845400-52846200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr20:52845400-52846200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:52845600-52847800	Enhancers	Fetal Lung	lung
14	chr20:52845800-52846200	Enhancers	HSMM	muscle

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