Variant report

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10810512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810525	0.88[CEU][hapmap]
rs10962252	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169479	0.81[CEU][hapmap]
rs11790527	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11792622	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328271	0.83[AMR][1000 genomes]
rs13298860	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13298936	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16933965	0.85[ASN][1000 genomes]
rs17352900	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17353213	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2794636	0.82[CEU][hapmap]
rs2987071	0.85[CEU][hapmap]
rs2987090	0.88[AMR][1000 genomes]
rs2987098	0.84[AMR][1000 genomes]
rs3008714	0.84[AMR][1000 genomes]
rs66532067	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031840	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs770211	0.81[CEU][hapmap]
rs770213	0.82[CEU][hapmap]
rs9407712	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10962251	PLP1	trans	parietal	SCAN
rs10962251	NUMA1	trans	parietal	SCAN
rs10962251	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16002400-16012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:16010400-16013400	Enhancers	Osteobl	bone
3	chr9:16011000-16014000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:16011800-16013000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:16011800-16013200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:16011800-16013200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:16011800-16013200	Enhancers	NHDF-Ad	bronchial
8	chr9:16012000-16013400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr9:16012000-16013600	Enhancers	NH-A	brain
10	chr9:16012200-16013000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:16012200-16013200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:16012200-16013200	Enhancers	A549	lung

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