Variant report

Variant	rs1026888
Chromosome Location	chr3:43501399-43501400
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10510737	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17075754	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1842805	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2372435	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441778	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772068	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6795944	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6800306	0.92[YRI][hapmap]
rs6802567	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72865005	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72865013	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72865025	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72865027	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72865029	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636753	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7651078	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs922642	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9758468	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9758483	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1026888	SNRK	cis	cerebellum	SCAN
rs1026888	PTH1R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43473400-43541400	Weak transcription	Aorta	Aorta
2	chr3:43474200-43504400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:43492600-43504200	Weak transcription	Fetal Intestine Small	intestine
4	chr3:43494600-43504200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:43496000-43509000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:43496800-43504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:43496800-43509400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:43497000-43504200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:43497000-43504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:43497000-43504200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:43497000-43504200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:43497000-43507000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:43497000-43514800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:43497000-43514800	Weak transcription	Gastric	stomach
15	chr3:43497000-43539400	Weak transcription	HSMM	muscle
16	chr3:43497200-43503000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:43497200-43504200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:43497200-43506000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:43497200-43519600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:43497200-43520000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:43497200-43532600	Weak transcription	K562	blood
22	chr3:43498800-43504200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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