Variant report

Variant	rs13089059
Chromosome Location	chr3:155383148-155383149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155379377..155381344-chr3:155382651..155384726,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1005736	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1007920	0.81[ASN][1000 genomes]
rs10936013	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12486000	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs12488043	0.81[ASN][1000 genomes]
rs12488087	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12490748	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12493067	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs13076587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082287	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13084995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087389	0.86[ASN][1000 genomes]
rs13095140	0.81[ASN][1000 genomes]
rs1519532	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1519533	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1519534	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1519535	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568360	0.81[ASN][1000 genomes]
rs168601	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs173384	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1835212	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs1879090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879091	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879092	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2203886	0.86[ASN][1000 genomes]
rs2222275	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435194	0.82[JPT][hapmap]
rs34810038	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358704	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs358706	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs358707	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs358708	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs358710	0.81[JPT][hapmap]
rs358711	0.81[JPT][hapmap]
rs358712	0.82[JPT][hapmap]
rs358727	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs358728	0.81[AMR][1000 genomes]
rs358732	0.88[MEX][hapmap]
rs358742	0.84[MEX][hapmap]
rs358896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358897	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358899	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358902	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs358904	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358905	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358906	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358910	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs359541	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs359543	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs359545	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs359546	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs359560	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs359567	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs378905	0.82[JPT][hapmap]
rs386867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392521	0.82[JPT][hapmap]
rs394419	0.82[JPT][hapmap]
rs407212	0.84[ASN][1000 genomes]
rs4083041	0.87[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412664	0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs417877	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs426069	0.86[ASN][1000 genomes]
rs430008	0.82[JPT][hapmap]
rs446716	0.82[JPT][hapmap]
rs448062	0.82[JPT][hapmap]
rs4679748	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs498378	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs592982	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs597718	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs60592119	0.81[ASN][1000 genomes]
rs629698	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs6441000	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6441006	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67428377	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772682	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6777741	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs67955071	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808257	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs687462	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7428196	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7645831	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13089059	SLC33A1	cis	cerebellum	SCAN
rs13089059	SMC4	cis	cerebellum	SCAN
rs13089059	PLCH1	cis	cerebellum	SCAN
rs13089059	SLC33A1	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155378800-155385400	Enhancers	Fetal Intestine Large	intestine
2	chr3:155380000-155383200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:155380400-155383400	Enhancers	Brain Germinal Matrix	brain
4	chr3:155381200-155383400	Enhancers	Fetal Stomach	stomach
5	chr3:155381200-155383400	Flanking Active TSS	A549	lung
6	chr3:155381200-155386200	Enhancers	Fetal Intestine Small	intestine
7	chr3:155381600-155383600	Enhancers	Small Intestine	intestine
8	chr3:155381800-155383200	Enhancers	Brain Hippocampus Middle	brain
9	chr3:155381800-155383400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:155382000-155383200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:155382000-155383400	Enhancers	Colon Smooth Muscle	Colon
12	chr3:155382000-155383600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:155382200-155383400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:155382200-155383400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:155382400-155383200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:155382400-155384200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:155382600-155383200	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr3:155382600-155383400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:155382600-155383400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:155382600-155383400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:155382600-155383400	Enhancers	Brain Anterior Caudate	brain
22	chr3:155382600-155383400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr3:155382600-155383400	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:155382800-155383200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:155382800-155383200	Enhancers	Fetal Muscle Leg	muscle
26	chr3:155382800-155383200	Enhancers	Ovary	ovary
27	chr3:155382800-155383200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr3:155382800-155383200	Enhancers	K562	blood
29	chr3:155382800-155383200	Enhancers	NHEK	skin
30	chr3:155382800-155383200	Enhancers	NHLF	lung
31	chr3:155382800-155383200	Enhancers	Osteobl	bone
32	chr3:155382800-155383400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:155382800-155383400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:155382800-155383400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:155382800-155383400	Enhancers	H9 Cell Line	embryonic stem cell
36	chr3:155382800-155383400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:155382800-155383400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:155382800-155383400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:155382800-155383400	Enhancers	Adipose Nuclei	Adipose
40	chr3:155382800-155383400	Enhancers	Colonic Mucosa	Colon
41	chr3:155382800-155383400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr3:155382800-155383400	Flanking Active TSS	HepG2	liver
43	chr3:155382800-155383400	Enhancers	HSMM	muscle
44	chr3:155382800-155383400	Enhancers	HSMMtube	muscle
45	chr3:155382800-155383400	Enhancers	NHDF-Ad	bronchial
46	chr3:155382800-155383600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:155382800-155383600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:155382800-155383600	Enhancers	Pancreas	Pancrea
49	chr3:155382800-155385200	Enhancers	Stomach Mucosa	stomach
50	chr3:155383000-155383200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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