Variant report

Variant	rs2023531
Chromosome Location	chr20:52893244-52893245
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52892973..52894968-chr20:52956980..52958556,2	MCF-7	breast:
2	chr20:52891151..52893259-chr21:33433759..33435627,2	MCF-7	breast:
3	chr20:52892335..52894745-chr20:52921772..52923928,2	MCF-7	breast:
4	chr20:52891210..52894147-chr20:52899496..52901678,2	MCF-7	breast:
5	chr20:52891755..52894002-chr3:64171405..64173308,2	MCF-7	breast:
6	chr20:52891578..52893729-chr20:52943256..52945368,2	MCF-7	breast:
7	chr20:52891487..52895363-chr20:52902222..52905146,4	MCF-7	breast:
8	chr20:52891107..52893591-chr20:52960404..52961944,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13039589	0.81[EUR][1000 genomes]
rs13039601	0.81[EUR][1000 genomes]
rs13042527	0.83[EUR][1000 genomes]
rs13045683	0.83[EUR][1000 genomes]
rs1477725	0.87[EUR][1000 genomes]
rs1477736	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs17223034	0.89[MEX][hapmap]
rs1964861	0.86[CEU][hapmap]
rs28404865	0.89[EUR][1000 genomes]
rs28435070	0.83[EUR][1000 genomes]
rs28526259	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28676447	0.82[EUR][1000 genomes]
rs28707344	0.83[EUR][1000 genomes]
rs28795767	0.93[EUR][1000 genomes]
rs292129	0.91[EUR][1000 genomes]
rs6013946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6023080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6023083	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	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
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv178887	chr20:52885413-52894836	Enhancers Weak transcription	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2023531	PFDN4	cis	parietal	SCAN
rs2023531	DOK5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52891800-52893800	Enhancers	Stomach Mucosa	stomach
2	chr20:52892800-52894000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr20:52893200-52894000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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