Variant report

Variant	rs57897477
Chromosome Location	chr15:52042710-52042711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52041917-52044815	Raji	blood:	n/a	n/a
2	POLR2A	chr15:52042188-52043672	GM12891	blood:	n/a	n/a
3	RELA	chr15:52042201-52043746	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
2	chr15:52041956..52043686-chr15:52074164..52076601,2	MCF-7	breast:
3	chr15:52029591..52032408-chr15:52042418..52044684,3	K562	blood:
4	chr15:52016515..52018648-chr15:52040542..52043046,2	MCF-7	breast:
5	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
6	chr15:52033609..52037215-chr15:52040115..52042966,3	MCF-7	breast:
7	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

No data

No data

No data

Variant related genes	Relation type
TMOD2	TF binding region
ENSG00000259377	TF binding region
ENSG00000128872	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2198804	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3751593	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3985808	1.00[AMR][1000 genomes]
rs56903771	1.00[AMR][1000 genomes]
rs58370000	1.00[AMR][1000 genomes]
rs58471786	1.00[AMR][1000 genomes]
rs58601413	1.00[AMR][1000 genomes]
rs59784585	1.00[AMR][1000 genomes]
rs60409555	1.00[AMR][1000 genomes]
rs60700084	1.00[AMR][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	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52030600-52043200	Weak transcription	Gastric	stomach
2	chr15:52031200-52043000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52041600-52042800	Enhancers	K562	blood
4	chr15:52042200-52043000	Enhancers	Primary B cells from peripheral blood	blood
5	chr15:52042600-52042800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr15:52042600-52043000	Enhancers	Brain Angular Gyrus	brain
7	chr15:52042600-52043000	Enhancers	Brain Cingulate Gyrus	brain
8	chr15:52042600-52043000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr15:52042600-52043000	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr15:52042600-52043200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:52042600-52043400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:52042600-52043600	Flanking Active TSS	GM12878-XiMat	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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