Variant report

Variant	rs10090944
Chromosome Location	chr8:110141670-110141671
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	chr8:110136298..110138304-chr8:110140145..110142017,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10087444	0.88[ASN][1000 genomes]
rs10505126	0.85[ASN][1000 genomes]
rs10955505	0.85[ASN][1000 genomes]
rs11778370	0.85[ASN][1000 genomes]
rs12543246	0.84[ASN][1000 genomes]
rs12680028	0.83[ASN][1000 genomes]
rs1458923	0.84[ASN][1000 genomes]
rs1531298	0.84[ASN][1000 genomes]
rs1947629	0.84[ASN][1000 genomes]
rs1993594	0.83[ASN][1000 genomes]
rs2125511	0.84[ASN][1000 genomes]
rs2125513	0.83[ASN][1000 genomes]
rs2926195	0.84[ASN][1000 genomes]
rs2926196	0.84[ASN][1000 genomes]
rs2926197	0.84[ASN][1000 genomes]
rs2926208	0.84[ASN][1000 genomes]
rs2926214	0.84[ASN][1000 genomes]
rs2926269	0.82[ASN][1000 genomes]
rs2926277	0.82[ASN][1000 genomes]
rs2980589	0.84[ASN][1000 genomes]
rs2980591	0.84[ASN][1000 genomes]
rs2980602	0.83[ASN][1000 genomes]
rs2980606	0.83[ASN][1000 genomes]
rs2980611	0.82[ASN][1000 genomes]
rs2980619	0.82[ASN][1000 genomes]
rs2980620	0.82[ASN][1000 genomes]
rs2980621	0.82[ASN][1000 genomes]
rs3925088	0.82[ASN][1000 genomes]
rs4129682	0.83[ASN][1000 genomes]
rs4236802	0.85[ASN][1000 genomes]
rs4301422	0.85[ASN][1000 genomes]
rs4342559	0.85[ASN][1000 genomes]
rs4734193	0.84[ASN][1000 genomes]
rs4734194	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734195	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734206	0.86[ASN][1000 genomes]
rs4735091	0.83[ASN][1000 genomes]
rs4735094	0.85[ASN][1000 genomes]
rs4735117	0.88[ASN][1000 genomes]
rs4735119	0.88[ASN][1000 genomes]
rs56247307	0.90[ASN][1000 genomes]
rs6469235	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469241	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6469248	0.84[ASN][1000 genomes]
rs6469249	0.84[ASN][1000 genomes]
rs6996836	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7003376	0.90[ASN][1000 genomes]
rs7003806	0.90[ASN][1000 genomes]
rs7009169	0.92[ASN][1000 genomes]
rs7012304	0.92[ASN][1000 genomes]
rs7819201	0.89[ASN][1000 genomes]
rs7821463	0.83[ASN][1000 genomes]
rs7839867	0.90[ASN][1000 genomes]
rs7840000	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022273	chr8:110026712-110146600	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv539715	chr8:110026712-110146600	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10090944	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110121400-110144600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:110138400-110142600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr8:110139600-110142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:110140400-110142400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:110140800-110142200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr8:110141200-110142000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:110141200-110142400	Enhancers	Hela-S3	cervix
8	chr8:110141200-110142400	Enhancers	Osteobl	bone
9	chr8:110141600-110142400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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