Variant report

Variant	rs386867
Chromosome Location	chr3:155394182-155394183
allele	C/G
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	TCF7L2	chr3:155394023-155394461	HEK293	kidney:	n/a	chr3:155394237-155394253 chr3:155394237-155394253
2	FOS	chr3:155394117-155394344	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr3:155394085-155394361	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr3:155394010-155394357	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr3:155394040-155394190	HMEC	breast:	n/a	n/a
6	KAP1	chr3:155393883-155394622	HEK293	kidney:	n/a	n/a
7	POLR2A	chr3:155394073-155394291	H1-hESC	embryonic stem cell:	n/a	n/a
8	KAP1	chr3:155393945-155394532	U2OS	brain:	n/a	n/a
9	POLR2A	chr3:155393931-155394566	H1-neurons	neurons:	n/a	n/a
10	MAX	chr3:155393999-155394301	SK-N-SH	brain:	n/a	n/a
11	FOXP2	chr3:155394017-155394369	PFSK-1	brain:	n/a	n/a
12	MXI1	chr3:155393704-155394866	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr3:155394089-155394196	Gliobla	brain:	n/a	n/a
14	POLR2A	chr3:155393986-155394527	H1-neurons	neurons:	n/a	n/a
15	E2F4	chr3:155394168-155394536	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr3:155393886-155394569	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr3:155394087-155394411	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr3:155394123-155394286	MCF10A-Er-Src	breast:	n/a	n/a
19	GATA2	chr3:155393889-155394430	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
PLCH1	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

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];0.82[AMR][1000 genomes]
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];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082287	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13084995	1.00[AMR][1000 genomes];1.00[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];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]
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	0.86[JPT][hapmap]
rs1879090	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]
rs1879091	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879092	0.97[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];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[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];0.98[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];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[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]
rs358896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358897	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358899	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358902	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358906	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358910	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[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];0.82[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]
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];0.99[ASN][1000 genomes]
rs412664	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs417877	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[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[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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];0.80[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];0.81[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

No data

Chromatin state (count:62 , 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	chr3:155393000-155394400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:155393200-155394200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:155393200-155394600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:155393200-155395000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:155393400-155394600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:155393800-155394200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
9	chr3:155393800-155394200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:155393800-155394200	Active TSS	Brain Hippocampus Middle	brain
11	chr3:155393800-155394200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr3:155393800-155394200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:155393800-155394200	Active TSS	Fetal Brain Female	brain
14	chr3:155393800-155394200	Flanking Active TSS	Fetal Intestine Large	intestine
15	chr3:155393800-155394200	Active TSS	Right Ventricle	heart
16	chr3:155393800-155394400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:155393800-155394600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:155393800-155394600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:155393800-155394600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:155393800-155394600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr3:155393800-155394600	Active TSS	Brain Germinal Matrix	brain
22	chr3:155393800-155394600	Active TSS	Stomach Smooth Muscle	stomach
23	chr3:155393800-155394600	Active TSS	A549	lung
24	chr3:155393800-155394600	Enhancers	NHEK	skin
25	chr3:155393800-155394800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
26	chr3:155393800-155394800	Active TSS	Brain Anterior Caudate	brain
27	chr3:155393800-155394800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:155393800-155395000	Enhancers	Stomach Mucosa	stomach
29	chr3:155394000-155394200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:155394000-155394200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:155394000-155394200	Active TSS	Duodenum Mucosa	Duodenum
32	chr3:155394000-155394200	Active TSS	Fetal Kidney	kidney
33	chr3:155394000-155394200	Active TSS	Ovary	ovary
34	chr3:155394000-155394200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:155394000-155394200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:155394000-155394200	Enhancers	NH-A	brain
37	chr3:155394000-155394200	Active TSS	NHDF-Ad	bronchial
38	chr3:155394000-155394400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:155394000-155394400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:155394000-155394400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:155394000-155394400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:155394000-155394400	Active TSS	Fetal Intestine Small	intestine
43	chr3:155394000-155394400	Active TSS	Gastric	stomach
44	chr3:155394000-155394400	Active TSS	Left Ventricle	heart
45	chr3:155394000-155394400	Active TSS	Pancreas	Pancrea
46	chr3:155394000-155394400	Flanking Active TSS	Psoas Muscle	Psoas
47	chr3:155394000-155394400	Flanking Active TSS	HMEC	breast
48	chr3:155394000-155394400	Active TSS	NHLF	lung
49	chr3:155394000-155394600	Enhancers	H9 Cell Line	embryonic stem cell
50	chr3:155394000-155394600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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