Variant report

Variant	rs12001383
Chromosome Location	chr9:16195440-16195441
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10962321	0.94[EUR][1000 genomes]
rs12002003	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12005826	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16934192	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16934196	0.88[EUR][1000 genomes]
rs16934202	0.98[EUR][1000 genomes]
rs16934204	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16934205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4076698	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56314211	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58894129	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61542621	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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	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
2	nsv429999	chr9:16102066-16389100	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv892639	chr9:16190403-16242088	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12001383	PRPF19	trans	parietal	SCAN
rs12001383	UBE2Z	trans	parietal	SCAN
rs12001383	MKRN1	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16185600-16196400	Weak transcription	Aorta	Aorta
2	chr9:16192400-16196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:16192400-16196800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:16192400-16197000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:16192400-16197200	Weak transcription	Psoas Muscle	Psoas
6	chr9:16192400-16197200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:16192600-16197000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:16192800-16196600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:16193000-16196400	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:16193200-16196000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:16193200-16196200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:16193400-16196000	Weak transcription	Fetal Stomach	stomach
13	chr9:16193400-16196600	Weak transcription	Fetal Lung	lung
14	chr9:16193400-16196800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:16193600-16196000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:16193600-16196200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:16193600-16196400	Weak transcription	HSMM	muscle
18	chr9:16193600-16196400	Weak transcription	NHDF-Ad	bronchial
19	chr9:16193600-16197800	Weak transcription	Placenta	Placenta
20	chr9:16193600-16202000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:16193600-16202200	Weak transcription	NHLF	lung
22	chr9:16193800-16196000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:16193800-16196000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:16193800-16196200	Weak transcription	Osteobl	bone
25	chr9:16193800-16196400	Weak transcription	HSMMtube	muscle
26	chr9:16193800-16196600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:16193800-16197000	Weak transcription	Ovary	ovary
28	chr9:16193800-16198200	Weak transcription	Fetal Kidney	kidney
29	chr9:16193800-16202000	Weak transcription	A549	lung
30	chr9:16194000-16196400	Weak transcription	NH-A	brain
31	chr9:16194200-16196000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:16194200-16196800	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:16195000-16197400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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