Variant report

Variant	rs1061409
Chromosome Location	chr3:145917761-145917762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13326891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398528	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398530	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1512889	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35418885	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762685	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762687	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804647	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804649	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4314144	0.91[CEU][hapmap];0.88[CHB][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681115	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57764107	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59965250	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792036	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792166	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6792604	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6804987	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7611293	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611299	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7611459	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611582	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633567	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9809574	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9814972	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9821768	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830885	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838816	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9840954	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9844172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854377	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854697	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9870547	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9870686	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9870699	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874112	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874234	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876826	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9880432	0.97[EUR][1000 genomes];0.96[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1061409	PFN2	cis	cerebellum	SCAN
rs1061409	PLSCR4	cis	parietal	SCAN
rs1061409	PLSCR4	cis	Adipose Subcutaneous	GTEx
rs1061409	PLSCR4	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145895800-145918200	Weak transcription	NHDF-Ad	bronchial
2	chr3:145897000-145933600	Weak transcription	Fetal Stomach	stomach
3	chr3:145901000-145923800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:145902800-145923000	Weak transcription	Osteobl	bone
5	chr3:145902800-145923600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:145903000-145934800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:145905000-145933600	Weak transcription	NHLF	lung
8	chr3:145907000-145938600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:145907400-145918200	Weak transcription	HepG2	liver
10	chr3:145907600-145939200	Weak transcription	Brain Anterior Caudate	brain
11	chr3:145908200-145936400	Weak transcription	A549	lung
12	chr3:145909600-145939200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:145910400-145932400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:145910400-145940000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:145912200-145923800	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:145912600-145923600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:145913200-145920200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:145913200-145920600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:145913200-145923200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:145913400-145920400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:145913800-145939200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:145914000-145923400	Weak transcription	Fetal Intestine Large	intestine
23	chr3:145914200-145920200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:145914200-145937000	Weak transcription	Placenta	Placenta
25	chr3:145914600-145940200	Weak transcription	Gastric	stomach
26	chr3:145914800-145918200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:145914800-145919200	Weak transcription	Left Ventricle	heart
28	chr3:145914800-145924200	Weak transcription	Aorta	Aorta
29	chr3:145914800-145940200	Weak transcription	Psoas Muscle	Psoas
30	chr3:145914800-145940400	Weak transcription	Spleen	Spleen
31	chr3:145915800-145917800	Strong transcription	Fetal Lung	lung
32	chr3:145916800-145918200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:145917000-145917800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:145917000-145917800	Enhancers	Fetal Heart	heart
35	chr3:145917000-145917800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:145917000-145917800	Strong transcription	HSMMtube	muscle
37	chr3:145917000-145917800	Strong transcription	HUVEC	blood vessel
38	chr3:145917000-145918600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:145917000-145918600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:145917000-145918800	Strong transcription	Liver	Liver
41	chr3:145917000-145919000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:145917000-145921400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:145917400-145917800	Strong transcription	Ovary	ovary
44	chr3:145917400-145918000	Strong transcription	Pancreas	Pancrea
45	chr3:145917400-145918800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr3:145917400-145925200	Strong transcription	Adipose Nuclei	Adipose
47	chr3:145917600-145917800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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