Variant report

Variant	rs10405856
Chromosome Location	chr19:52689461-52689462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52689327..52690920-chr19:52699885..52701616,2	MCF-7	breast:
2	chr19:52683661..52685603-chr19:52687711..52690241,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1025279	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10404867	0.88[ASN][1000 genomes]
rs10405103	0.88[ASN][1000 genomes]
rs10405293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405519	0.90[ASN][1000 genomes]
rs10405862	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10407987	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10410506	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10410908	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10411335	0.87[CEU][hapmap]
rs10411382	0.88[ASN][1000 genomes]
rs10412525	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10413274	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10413372	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10413470	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10413847	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10415203	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10416195	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422583	0.82[EUR][1000 genomes]
rs10423610	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10423794	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10424348	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10426066	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs13344984	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16983548	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16983549	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16983557	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1984750	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61435553	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7253157	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73935026	0.83[EUR][1000 genomes]
rs73937434	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8101364	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8103874	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs8107377	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking 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 miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10405856	PPP2R1A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52680200-52692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:52680400-52691800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:52688600-52691600	Weak transcription	Brain Anterior Caudate	brain

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