Variant report

Variant	rs7866652
Chromosome Location	chr9:108732469-108732470
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	chr9:108730359..108732528-chr9:108735716..108738516,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10733558	0.92[ASN][1000 genomes]
rs10759156	0.92[ASN][1000 genomes]
rs10816356	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs10978344	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10978345	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10978346	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10978361	0.90[ASN][1000 genomes]
rs10978362	0.90[ASN][1000 genomes]
rs2417669	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2417670	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2417677	0.91[ASN][1000 genomes]
rs2417678	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2900407	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4076012	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[ASN][1000 genomes]
rs4336667	0.88[EUR][1000 genomes]
rs4387040	0.86[ASN][1000 genomes]
rs4609252	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs55721325	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55735471	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7865804	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1047166	chr9:108693810-108921872	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7866652	LPPR1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108726800-108736800	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:108728200-108732600	Enhancers	Fetal Brain Male	brain
3	chr9:108728800-108733800	Enhancers	Brain Cingulate Gyrus	brain
4	chr9:108729000-108736800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:108729400-108732800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:108729400-108733000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:108729600-108732800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:108729600-108732800	Enhancers	Brain Hippocampus Middle	brain
9	chr9:108729600-108733400	Enhancers	Brain Substantia Nigra	brain
10	chr9:108730000-108733600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr9:108730200-108732600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:108730200-108732800	Enhancers	Brain Angular Gyrus	brain
13	chr9:108730800-108733000	Enhancers	Brain Anterior Caudate	brain
14	chr9:108731400-108732600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:108731400-108732600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:108731600-108732600	Enhancers	Fetal Brain Female	brain
17	chr9:108731600-108732800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:108731800-108734800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:108732200-108732600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:108732200-108733200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:108732200-108741000	Weak transcription	Brain Germinal Matrix	brain
22	chr9:108732400-108738400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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