Variant report

Variant	rs6023406
Chromosome Location	chr20:53219961-53219962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52836031..52836766-chr20:53219732..53220485,2	MCF-7	breast:
2	chr20:53218785..53221076-chr3:64335798..64337803,2	MCF-7	breast:
3	chr20:53218462..53220917-chr20:53263377..53265971,2	MCF-7	breast:
4	chr20:53201780..53208417-chr20:53214130..53221252,9	MCF-7	breast:
5	chr20:53219603..53221851-chr20:53222330..53224906,2	MCF-7	breast:
6	chr20:53212235..53214579-chr20:53217429..53220082,3	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs13040265	1.00[CHD][hapmap]
rs1569985	1.00[CHD][hapmap]
rs16999872	1.00[ASN][1000 genomes]
rs1983702	1.00[CHD][hapmap]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[CHD][hapmap]
rs2224269	1.00[CHD][hapmap]
rs28663252	1.00[ASN][1000 genomes]
rs2870331	1.00[ASN][1000 genomes]
rs2870332	1.00[ASN][1000 genomes]
rs2870333	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs2904386	1.00[ASN][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4324376	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334548	1.00[CHD][hapmap]
rs4542911	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581960	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4809968	1.00[ASN][1000 genomes]
rs4809969	1.00[CHD][hapmap]
rs4811510	1.00[ASN][1000 genomes]
rs4811511	1.00[ASN][1000 genomes]
rs4811513	1.00[ASN][1000 genomes]
rs4996783	1.00[ASN][1000 genomes]
rs58298733	1.00[ASN][1000 genomes]
rs60030360	1.00[ASN][1000 genomes]
rs6014078	1.00[ASN][1000 genomes]
rs6014080	1.00[ASN][1000 genomes]
rs6014081	0.81[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs6014106	1.00[CHD][hapmap]
rs6023367	1.00[CHD][hapmap]
rs6023397	1.00[ASN][1000 genomes]
rs6023398	1.00[ASN][1000 genomes]
rs6023400	1.00[ASN][1000 genomes]
rs6023401	1.00[ASN][1000 genomes]
rs6023403	1.00[ASN][1000 genomes]
rs6023407	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6023408	1.00[ASN][1000 genomes]
rs6023409	1.00[ASN][1000 genomes]
rs6023410	1.00[ASN][1000 genomes]
rs6023423	1.00[CHD][hapmap]
rs6023428	1.00[ASN][1000 genomes]
rs6023429	1.00[CHD][hapmap]
rs6023430	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6023474	1.00[CHD][hapmap]
rs6064093	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6064102	1.00[CHD][hapmap]
rs6068916	1.00[ASN][1000 genomes]
rs6068920	1.00[ASN][1000 genomes]
rs6068924	1.00[CHD][hapmap]
rs6091928	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091931	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6098103	1.00[ASN][1000 genomes]
rs6098105	1.00[ASN][1000 genomes]
rs6098108	1.00[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs6098120	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6098158	1.00[CHD][hapmap]
rs6123404	1.00[CHD][hapmap]
rs7261209	1.00[ASN][1000 genomes]
rs7263678	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7263680	1.00[ASN][1000 genomes]
rs7269966	1.00[ASN][1000 genomes]
rs7270451	1.00[CHD][hapmap]
rs7270971	1.00[CHD][hapmap]
rs8115071	1.00[CHD][hapmap]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs967377	1.00[CHD][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[ASN][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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6023406	PMEPA1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53202200-53230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
3	chr20:53206400-53226600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:53215200-53236400	Weak transcription	Aorta	Aorta
5	chr20:53216400-53227000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:53216800-53226800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:53217000-53225800	Weak transcription	Fetal Brain Female	brain
8	chr20:53217000-53235800	Weak transcription	Brain Germinal Matrix	brain
9	chr20:53217400-53222000	Weak transcription	Psoas Muscle	Psoas
10	chr20:53217400-53240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:53217800-53226200	Weak transcription	Fetal Brain Male	brain
12	chr20:53217800-53227000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr20:53217800-53227400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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