Variant report

Variant	rs1879090
Chromosome Location	chr3:155394481-155394482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:155393883-155394622	HEK293	kidney:	n/a	n/a
2	KAP1	chr3:155393945-155394532	U2OS	brain:	n/a	n/a
3	POLR2A	chr3:155393931-155394566	H1-neurons	neurons:	n/a	n/a
4	MXI1	chr3:155393704-155394866	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:155393986-155394527	H1-neurons	neurons:	n/a	n/a
6	E2F4	chr3:155394168-155394536	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr3:155393886-155394569	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PLCH1	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1005736	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1007920	0.80[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]
rs12488043	0.80[ASN][1000 genomes]
rs12488087	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082287	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13084995	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087389	0.85[ASN][1000 genomes]
rs13089059	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]
rs13095140	0.80[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	0.80[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]
rs1879091	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879092	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2203886	0.85[ASN][1000 genomes]
rs2222275	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435194	0.82[JPT][hapmap]
rs34810038	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs358732	0.83[MEX][hapmap]
rs358742	0.89[MEX][hapmap]
rs358896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358897	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358898	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358899	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358902	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs358904	0.90[AMR][1000 genomes];0.91[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];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358906	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358910	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358912	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];1.00[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];0.89[MEX][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	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412664	0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs417877	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426069	0.87[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	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67428377	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772682	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6777741	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs67955071	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808257	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs687462	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7428196	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7645831	0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[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
rs1879090	SLC33A1	cis	cerebellum	SCAN
rs1879090	PLCH1	cis	cerebellum	SCAN
rs1879090	SLC33A1	cis	parietal	SCAN
rs1879090	IPO13	trans	brain	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155383400-155395800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:155392800-155394600	Active TSS	Right Atrium	heart
3	chr3:155393200-155394600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:155393200-155395000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:155393400-155394600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:155393800-155394600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:155393800-155394600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:155393800-155394600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:155393800-155394600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr3:155393800-155394600	Active TSS	Brain Germinal Matrix	brain
11	chr3:155393800-155394600	Active TSS	Stomach Smooth Muscle	stomach
12	chr3:155393800-155394600	Active TSS	A549	lung
13	chr3:155393800-155394600	Enhancers	NHEK	skin
14	chr3:155393800-155394800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
15	chr3:155393800-155394800	Active TSS	Brain Anterior Caudate	brain
16	chr3:155393800-155394800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:155393800-155395000	Enhancers	Stomach Mucosa	stomach
18	chr3:155394000-155394600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:155394000-155394600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:155394000-155394600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:155394000-155394600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:155394000-155394600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:155394000-155394600	Active TSS	Brain Cingulate Gyrus	brain
24	chr3:155394000-155394600	Active TSS	Fetal Brain Male	brain
25	chr3:155394000-155394600	Flanking Active TSS	Fetal Lung	lung
26	chr3:155394000-155394600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:155394000-155394600	Active TSS	HepG2	liver
28	chr3:155394000-155394800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:155394000-155394800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:155394000-155394800	Active TSS	Brain Angular Gyrus	brain
31	chr3:155394000-155394800	Active TSS	Brain Substantia Nigra	brain
32	chr3:155394200-155394600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:155394200-155394600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:155394200-155394600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:155394200-155394600	Active TSS	Liver	Liver
36	chr3:155394200-155394600	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr3:155394200-155394600	Enhancers	Fetal Heart	heart
38	chr3:155394200-155394600	Active TSS	Fetal Intestine Large	intestine
39	chr3:155394200-155394600	Flanking Active TSS	Ovary	ovary
40	chr3:155394200-155394600	Active TSS	Rectal Smooth Muscle	rectum
41	chr3:155394200-155394600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:155394200-155394600	Flanking Active TSS	NH-A	brain
43	chr3:155394200-155394600	Flanking Active TSS	NHDF-Ad	bronchial
44	chr3:155394200-155394800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr3:155394200-155394800	Active TSS	Colon Smooth Muscle	Colon
46	chr3:155394200-155394800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:155394200-155394800	Flanking Active TSS	Fetal Kidney	kidney
48	chr3:155394400-155394600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:155394400-155394600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
50	chr3:155394400-155394600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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