Variant report

Variant	rs16999560
Chromosome Location	chr20:52984616-52984617
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:49347789..49349298-chr20:52984375..52987184,2	MCF-7	breast:
2	chr20:52979804..52981716-chr20:52983200..52985662,2	MCF-7	breast:
3	chr20:52983863..52986994-chr20:52995623..52998239,3	MCF-7	breast:
4	chr20:49347583..49351619-chr20:52982625..52987672,5	MCF-7	breast:
5	chr20:52982598..52985363-chr20:52985830..52988598,3	MCF-7	breast:
6	chr20:52983415..52985850-chr6:27858765..27861037,2	MCF-7	breast:
7	chr17:73511489..73512024-chr20:52984570..52985199,2	MCF-7	breast:
8	chr20:52981982..52984941-chr20:53255246..53257720,2	MCF-7	breast:
9	chr20:52977120..52978918-chr20:52982695..52985421,2	MCF-7	breast:
10	chr20:52982179..52987061-chr20:52989270..52993345,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000177303	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1321464	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1321465	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs1321468	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1358806	0.81[EUR][1000 genomes]
rs1539515	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17224616	0.94[EUR][1000 genomes]
rs17224715	0.96[EUR][1000 genomes]
rs17317237	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1923118	0.81[EUR][1000 genomes]
rs2126675	0.84[EUR][1000 genomes]
rs2126677	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2870329	0.81[EUR][1000 genomes]
rs55865213	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56339826	1.00[EUR][1000 genomes]
rs6013997	0.81[EUR][1000 genomes]
rs6014005	0.81[EUR][1000 genomes]
rs6014011	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs6023193	0.81[EUR][1000 genomes]
rs6023227	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs6091858	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6091860	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097931	0.96[EUR][1000 genomes]
rs6097942	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6097943	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6097944	0.87[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6097950	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097957	0.81[EUR][1000 genomes]
rs6097964	0.81[EUR][1000 genomes]
rs6097967	0.81[EUR][1000 genomes]
rs73143321	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73143323	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73145242	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73145250	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73145257	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73145263	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73145271	0.90[EUR][1000 genomes]
rs73145273	1.00[EUR][1000 genomes]
rs73145277	1.00[EUR][1000 genomes]
rs73147267	0.90[EUR][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	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
2	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52976600-52985200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr20:52977600-52985200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:52977800-52985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr20:52979200-52984800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr20:52983400-52986200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr20:52983800-52985200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:52984200-52985000	Enhancers	H9 Cell Line	embryonic stem cell
8	chr20:52984600-52986000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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