Variant report

Variant	rs208368
Chromosome Location	chr20:52599243-52599244
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: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	chr20:52599104..52600037-chr20:52811545..52812537,13	MCF-7	breast:
2	chr10:123469862..123471363-chr20:52598792..52600401,2	MCF-7	breast:
3	chr20:52598102..52600086-chr9:140203803..140205812,2	MCF-7	breast:
4	chr17:56716862..56717700-chr20:52599173..52599748,3	MCF-7	breast:
5	chr20:52596990..52599653-chr7:102503790..102506770,2	MCF-7	breast:
6	chr20:52599220..52600148-chr20:52765356..52766212,6	MCF-7	breast:
7	chr20:52599179..52599997-chr20:52811545..52812537,5	MCF-7	breast:
8	chr20:52599220..52600094-chr20:52765356..52766214,8	MCF-7	breast:
9	chr20:52599185..52600133-chr20:52739769..52740826,4	MCF-7	breast:
10	chr20:52599136..52600133-chr20:52739769..52740911,9	MCF-7	breast:
11	chr20:52595597..52599294-chr20:52683836..52687749,4	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs119069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs119071	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs169639	0.81[YRI][hapmap]
rs208360	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs208371	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs208380	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208389	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2158977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390573	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs393744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6013869	0.81[EUR][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:10 , 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	chr20:52592000-52599600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr20:52592800-52599600	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:52593000-52600800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:52593200-52601000	Weak transcription	Brain Substantia Nigra	brain
8	chr20:52596400-52601400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:52597000-52599800	Weak transcription	HSMMtube	muscle
10	chr20:52597600-52601000	Weak transcription	Fetal Stomach	stomach

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

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