Variant report

Variant	rs1039286
Chromosome Location	chr1:197870310-197870311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:197870139-197873102	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:197870118-197872970	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197742347..197745266-chr1:197870109..197873225,5	MCF-7	breast:
2	chr1:197869855..197872200-chr1:198125548..198128117,2	MCF-7	breast:
3	chr1:197852642..197855916-chr1:197868509..197871754,4	K562	blood:
4	chr1:197854984..197856657-chr1:197868771..197871042,2	MCF-7	breast:
5	chr1:197837094..197838066-chr1:197870113..197870986,2	MCF-7	breast:
6	chr1:197846538..197849323-chr1:197868745..197871219,2	K562	blood:
7	chr1:197870101..197873220-chr1:197881150..197886265,4	MCF-7	breast:
8	chr1:197868383..197873929-chr1:197879774..197886951,11	K562	blood:
9	chr1:197589072..197591210-chr1:197869389..197871668,2	MCF-7	breast:
10	chr1:197740776..197744504-chr1:197869951..197872253,3	K562	blood:

No data

No data

No data

Variant related genes	Relation type
C1orf53	TF binding region
ENSG00000213047	Chromatin interaction
ENSG00000151414	Chromatin interaction
ENSG00000143355	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10733088	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1472498	0.90[ASW][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1499594	1.00[AMR][1000 genomes]
rs1499595	1.00[AMR][1000 genomes]
rs1580811	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1747819	0.90[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1775455	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2221133	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2477062	0.90[ASW][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2488399	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4628536	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915247	1.00[AMR][1000 genomes]
rs4915252	0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915571	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700740	0.81[AFR][1000 genomes]
rs7518074	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs953508	1.00[AMR][1000 genomes]
rs957939	0.85[AFR][1000 genomes];1.00[AMR][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	nsv999662	chr1:197821769-197892803	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	esv2762214	chr1:197821769-197897496	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv1004130	chr1:197822757-197879728	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197867200-197870800	Weak transcription	Rectal Smooth Muscle	rectum

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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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