Variant report

Variant	rs59965250
Chromosome Location	chr3:145943384-145943385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1061409	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13326891	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398526	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398528	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398530	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418885	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762685	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762687	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804647	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804649	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314144	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57294001	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57764107	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792036	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792166	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792604	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804987	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611293	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611299	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7611459	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611582	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633567	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809574	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814972	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821768	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830885	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838816	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840954	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844172	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849036	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850144	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854697	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870547	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870686	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870699	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874072	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874112	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874234	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876826	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9876833	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880432	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59965250	PLSCR4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle
3	chr3:145925000-145945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
6	chr3:145932600-145943800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:145934600-145952200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:145936000-145945200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:145940600-145943600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:145940600-145944800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:145940600-145953000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:145940600-145953600	Weak transcription	NHDF-Ad	bronchial
13	chr3:145940800-145944000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:145940800-145944000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:145940800-145944400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:145940800-145944400	Weak transcription	Fetal Stomach	stomach
17	chr3:145940800-145945000	Weak transcription	Aorta	Aorta
18	chr3:145940800-145945000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:145940800-145945200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:145940800-145945200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:145941400-145944800	Weak transcription	Adipose Nuclei	Adipose
22	chr3:145941400-145944800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:145941400-145945000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:145941400-145945800	Weak transcription	NHLF	lung
25	chr3:145941400-145948400	Weak transcription	Osteobl	bone
26	chr3:145941600-145943400	Weak transcription	Lung	lung
27	chr3:145941600-145945000	Weak transcription	Ovary	ovary
28	chr3:145941600-145945000	Weak transcription	Pancreas	Pancrea
29	chr3:145941600-145946000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:145941600-145947000	Weak transcription	Right Atrium	heart
31	chr3:145941600-145952200	Weak transcription	Left Ventricle	heart
32	chr3:145941600-145952600	Weak transcription	Fetal Intestine Small	intestine
33	chr3:145941600-145954000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:145942000-145944800	Weak transcription	Liver	Liver
35	chr3:145942000-145947000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:145942200-145943800	Weak transcription	Fetal Lung	lung
37	chr3:145942200-145946800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:145942200-145953400	Weak transcription	HUVEC	blood vessel
39	chr3:145943200-145943600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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