Variant report

Variant	rs57138648
Chromosome Location	chr15:52829028-52829029
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	chr15:52819614..52823741-chr15:52828078..52832253,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11853179	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11853954	0.86[AMR][1000 genomes]
rs11854405	0.84[AMR][1000 genomes]
rs11854673	0.81[AMR][1000 genomes]
rs11854780	0.81[AMR][1000 genomes]
rs11855467	0.86[AMR][1000 genomes]
rs11856626	0.81[AMR][1000 genomes]
rs1693522	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1693525	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1693526	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693527	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17651623	0.81[AMR][1000 genomes]
rs17651631	0.81[AMR][1000 genomes]
rs17651692	0.81[AMR][1000 genomes]
rs2272283	0.81[AMR][1000 genomes]
rs2554888	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34099958	0.81[AMR][1000 genomes]
rs34388417	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4776054	0.84[AMR][1000 genomes]
rs55710656	0.81[AMR][1000 genomes]
rs55842353	0.81[AMR][1000 genomes]
rs55914546	0.81[AMR][1000 genomes]
rs55946989	0.84[AMR][1000 genomes]
rs56017964	0.81[AMR][1000 genomes]
rs56279946	0.81[AMR][1000 genomes]
rs56849428	0.81[AMR][1000 genomes]
rs57997370	0.81[AMR][1000 genomes]
rs59477983	0.81[AMR][1000 genomes]
rs61494501	0.81[AMR][1000 genomes]
rs66461265	0.81[AMR][1000 genomes]
rs66755651	0.84[AMR][1000 genomes]
rs67423475	0.86[AMR][1000 genomes]
rs67827251	0.81[AMR][1000 genomes]
rs72623987	0.81[AMR][1000 genomes]
rs72738592	0.83[ASN][1000 genomes]
rs9788691	0.81[AMR][1000 genomes]
rs9788777	0.81[AMR][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs57138648	ARPP19	cis	Nerve Tibial	GTEx
rs57138648	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs57138648	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs57138648	KIAA1370	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52822200-52839600	Weak transcription	Right Atrium	heart
2	chr15:52822800-52838400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:52827600-52837200	Weak transcription	A549	lung
4	chr15:52828600-52829800	Enhancers	Liver	Liver
5	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain

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