Variant report

Variant	rs12483016
Chromosome Location	chr21:16546125-16546126
allele	G/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:16504804..16505761-chr21:16545069..16546286,8	MCF-7	breast:
2	chr21:16545079..16546143-chr21:16581995..16583288,32	MCF-7	breast:
3	chr21:16434158..16440207-chr21:16535498..16546791,27	MCF-7	breast:
4	chr21:16545087..16546235-chr21:16571540..16572822,5	MCF-7	breast:
5	chr21:16545028..16546143-chr21:16581995..16583350,24	MCF-7	breast:
6	chr21:16545273..16546244-chr21:16571963..16572719,3	MCF-7	breast:
7	chr21:16377421..16378235-chr21:16545003..16546153,5	MCF-7	breast:
8	chr21:16543825..16546494-chr21:16577749..16579512,2	MCF-7	breast:
9	chr21:16545692..16547442-chr21:16556635..16559222,2	MCF-7	breast:
10	chr21:16545793..16547434-chr21:16571393..16572944,2	MCF-7	breast:
11	chr21:16544983..16547085-chr21:16581063..16583747,4	MCF-7	breast:
12	chr21:16538318..16540321-chr21:16546089..16547766,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction
ENSG00000236471	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11088311	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12373912	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482834	0.81[ASN][1000 genomes]
rs12483602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556283	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882963	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007783	0.86[ASN][1000 genomes]
rs2008843	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2142362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2823088	0.81[ASN][1000 genomes]
rs2823091	0.86[ASN][1000 genomes]
rs2823093	0.86[ASN][1000 genomes]
rs2823096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs2823106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823119	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896680	0.86[ASN][1000 genomes]
rs2896689	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778206	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55792425	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55797017	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55859143	0.81[ASN][1000 genomes]
rs62218221	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62218223	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62218224	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62218225	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62218995	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62218996	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741937	0.86[ASN][1000 genomes]
rs8128132	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990302	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv913413	chr21:16537728-16621859	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12483016	TSSC4	trans	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16545000-16546200	Enhancers	HepG2	liver
2	chr21:16545400-16546200	Enhancers	Fetal Intestine Large	intestine
3	chr21:16545600-16546600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr21:16546000-16546600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:16546000-16546600	Enhancers	Pancreas	Pancrea

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