Variant report

Variant	rs12005826
Chromosome Location	chr9:16196674-16196675
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10962321	0.91[EUR][1000 genomes]
rs12001383	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12002003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16934192	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16934196	0.84[EUR][1000 genomes]
rs16934202	0.88[EUR][1000 genomes]
rs16934204	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16934205	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4076698	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56314211	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58894129	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61542621	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7850515	0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12005826	MKRN1	trans	parietal	SCAN
rs12005826	UBE2Z	trans	parietal	SCAN
rs12005826	ARPP19	trans	parietal	SCAN
rs12005826	PRPF19	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16192400-16196800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr9:16192400-16197000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:16192400-16197200	Weak transcription	Psoas Muscle	Psoas
4	chr9:16192400-16197200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:16192600-16197000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:16193400-16196800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:16193600-16197800	Weak transcription	Placenta	Placenta
8	chr9:16193600-16202000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:16193600-16202200	Weak transcription	NHLF	lung
10	chr9:16193800-16197000	Weak transcription	Ovary	ovary
11	chr9:16193800-16198200	Weak transcription	Fetal Kidney	kidney
12	chr9:16193800-16202000	Weak transcription	A549	lung
13	chr9:16194200-16196800	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:16195000-16197400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:16196000-16196800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:16196000-16197000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:16196000-16197600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:16196000-16198400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:16196000-16198800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:16196000-16199800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:16196200-16197000	Enhancers	Stomach Smooth Muscle	stomach
22	chr9:16196200-16198200	Enhancers	Osteobl	bone
23	chr9:16196200-16198400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:16196400-16197200	Enhancers	HSMMtube	muscle
25	chr9:16196400-16197200	Enhancers	NHDF-Ad	bronchial
26	chr9:16196400-16197400	Enhancers	Aorta	Aorta
27	chr9:16196400-16197600	Enhancers	Colon Smooth Muscle	Colon
28	chr9:16196400-16198200	Enhancers	NH-A	brain
29	chr9:16196400-16198400	Enhancers	HSMM	muscle
30	chr9:16196600-16197600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:16196600-16197600	Enhancers	Fetal Lung	lung
32	chr9:16196600-16198800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:16196600-16198800	Enhancers	Fetal Stomach	stomach
34	chr9:16196600-16198800	Enhancers	Left Ventricle	heart

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