Variant report

Variant	rs2299729
Chromosome Location	chr20:52596408-52596409
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52596205..52597011-chr20:52765364..52765924,2	MCF-7	breast:
2	chr20:52596225..52596747-chr20:52743745..52744250,2	MCF-7	breast:
3	chr10:63845311..63847924-chr20:52594546..52597386,2	MCF-7	breast:
4	chr20:52596286..52597038-chr20:52811502..52812174,4	MCF-7	breast:
5	chr20:52596286..52596804-chr20:52811617..52812118,2	MCF-7	breast:
6	chr17:56716851..56717594-chr20:52596237..52597195,2	MCF-7	breast:
7	chr1:41067796..41070793-chr20:52595128..52597334,3	MCF-7	breast:
8	chr20:52596227..52596815-chr20:52739956..52740669,2	MCF-7	breast:
9	chr20:52595597..52599294-chr20:52683836..52687749,4	MCF-7	breast:
10	chr20:52594177..52596911-chr20:52824324..52827148,2	MCF-7	breast:
11	chr20:52596289..52597066-chr20:52740123..52740715,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11086446	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12625473	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299725	0.85[ASN][1000 genomes]
rs2299726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299728	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299731	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299735	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2870300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819589	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62207381	0.89[ASN][1000 genomes]
rs62207383	0.89[ASN][1000 genomes]
rs73137776	0.95[EUR][1000 genomes];0.90[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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52580800-52600000	Weak transcription	Stomach Mucosa	stomach
3	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52591200-52597000	Strong transcription	HSMMtube	muscle
5	chr20:52592000-52599600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:52592800-52599600	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:52593000-52600800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:52593200-52601000	Weak transcription	Brain Substantia Nigra	brain
9	chr20:52596000-52597400	Enhancers	Fetal Lung	lung
10	chr20:52596000-52597600	Enhancers	Fetal Stomach	stomach
11	chr20:52596200-52597200	Weak transcription	Placenta	Placenta
12	chr20:52596400-52601400	Weak transcription	Rectal Mucosa Donor 31	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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