Variant report

Variant	rs56128832
Chromosome Location	chr8:52663361-52663362
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52638232..52640953-chr8:52662899..52665475,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10097328	0.87[EUR][1000 genomes]
rs10102568	0.87[EUR][1000 genomes]
rs10504127	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12115132	0.87[EUR][1000 genomes]
rs16916903	0.87[EUR][1000 genomes]
rs16919843	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2020431	0.87[EUR][1000 genomes]
rs28635761	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28652885	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4873588	0.83[EUR][1000 genomes]
rs4873602	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873609	0.87[EUR][1000 genomes]
rs56394995	0.87[EUR][1000 genomes]
rs58408501	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58591247	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59344101	0.90[AFR][1000 genomes]
rs7008721	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7010217	0.81[EUR][1000 genomes]
rs73590413	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73592226	0.87[EUR][1000 genomes]
rs7843530	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv890898	chr8:52579964-52680933	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56128832	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52644000-52665400	Weak transcription	Right Ventricle	heart
2	chr8:52660800-52665200	Weak transcription	Fetal Kidney	kidney
3	chr8:52661200-52665000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:52661400-52666400	Weak transcription	Psoas Muscle	Psoas
5	chr8:52661400-52671400	Weak transcription	Right Atrium	heart
6	chr8:52661400-52683200	Weak transcription	Left Ventricle	heart
7	chr8:52661600-52664400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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