Variant report

Variant	rs3745002
Chromosome Location	chr18:43652345-43652346
allele	A/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	CBX3	chr18:43652075-43652418	K562	blood:	n/a	n/a
2	POLR2A	chr18:43651769-43652723	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF263	chr18:43651948-43652529	HEK293-T-REx	kidney:	n/a	n/a
4	MYC	chr18:43651658-43652416	MCF10A-Er-Src	breast:	n/a	chr18:43651886-43651893 chr18:43652044-43652053
5	ARID3A	chr18:43652166-43652366	K562	blood:	n/a	n/a
6	POLR2A	chr18:43652004-43652360	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr18:43652260-43652410	HMEC	breast:	n/a	chr18:43652279-43652289
8	RUNX3	chr18:43652044-43652476	GM12878	blood:	n/a	n/a
9	RCOR1	chr18:43651724-43652530	K562	blood:	n/a	n/a
10	POLR2A	chr18:43651743-43652486	GM19193	blood:	n/a	n/a
11	EP300	chr18:43652066-43652402	T-47D	breast:	n/a	n/a
12	NRF1	chr18:43651987-43652575	SK-N-SH	brain:	n/a	n/a
13	CTBP2	chr18:43651294-43652484	H1-hESC	embryonic stem cell:	n/a	n/a
14	IRF1	chr18:43652245-43652384	K562	blood:	n/a	n/a
15	ZMIZ1	chr18:43652134-43652374	K562	blood:	n/a	n/a
16	MYC	chr18:43651658-43652380	K562	blood:	n/a	chr18:43651886-43651893 chr18:43652044-43652053
17	POLR2A	chr18:43651891-43652743	SK-N-MC	brain:	n/a	n/a
18	ZBTB7A	chr18:43651141-43652680	ECC-1	luminal epithelium:	n/a	chr18:43651829-43651838
19	MAZ	chr18:43652270-43652470	HepG2	liver:	n/a	n/a
20	YY1	chr18:43652109-43652346	GM12891	blood:	n/a	n/a
21	RCOR1	chr18:43652299-43652399	K562	blood:	n/a	n/a
22	CTCF	chr18:43652300-43652450	Hela-S3	cervix:	n/a	n/a
23	ZNF143	chr18:43652091-43652551	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3A	chr18:43651592-43652518	H1-hESC	embryonic stem cell:	n/a	chr18:43651691-43651700 chr18:43651824-43651835 chr18:43652365-43652376
25	TAF1	chr18:43651976-43652496	GM12878	blood:	n/a	n/a
26	STAT5A	chr18:43651663-43652355	GM12878	blood:	n/a	n/a
27	POLR2A	chr18:43651820-43652574	GM12892	blood:	n/a	n/a
28	POLR2A	chr18:43652031-43652431	HUVEC	blood vessel:	n/a	n/a
29	TAF1	chr18:43652091-43652402	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr18:43652204-43652357	HepG2	liver:	n/a	n/a
31	MAZ	chr18:43652289-43652467	Hela-S3	cervix:	n/a	n/a
32	ZNF143	chr18:43652102-43652484	K562	blood:	n/a	n/a
33	FOSL1	chr18:43652054-43652542	K562	blood:	n/a	n/a
34	MAX	chr18:43651557-43652564	ECC-1	luminal epithelium:	n/a	chr18:43651886-43651893 chr18:43652044-43652053
35	GABPA	chr18:43652105-43652430	H1-hESC	embryonic stem cell:	n/a	n/a
36	UBTF	chr18:43651006-43652701	K562	blood:	n/a	n/a
37	EGR1	chr18:43652115-43652423	K562	blood:	n/a	n/a
38	ZNF384	chr18:43652187-43652387	K562	blood:	n/a	n/a
39	CTCF	chr18:43652304-43652482	GM12878	blood:	n/a	chr18:43652461-43652479 chr18:43652463-43652476
40	POLR2A	chr18:43651996-43652455	IMR90	lung:	n/a	n/a
41	TRIM28	chr18:43652066-43652375	K562	blood:	n/a	n/a
42	FOXP2	chr18:43652020-43652454	PFSK-1	brain:	n/a	n/a
43	CTCF	chr18:43652200-43652350	GM12874	blood:	n/a	chr18:43652279-43652289
44	POLR2A	chr18:43652027-43652452	PFSK-1	brain:	n/a	n/a
45	ZNF143	chr18:43652105-43652495	GM12878	blood:	n/a	n/a
46	YY1	chr18:43652095-43652357	K562	blood:	n/a	n/a
47	POLR2A	chr18:43652008-43652520	GM15510	blood:	n/a	n/a
48	HDAC2	chr18:43652193-43652433	K562	blood:	n/a	n/a
49	CTCF	chr18:43652260-43652410	SAEC	small airway:	n/a	chr18:43652279-43652289
50	CTCF	chr18:43652287-43652525	K562	blood:	n/a	chr18:43652461-43652479 chr18:43652463-43652476

Variant related genes	Relation type
PSTPIP2	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11876373	0.82[ASN][1000 genomes]
rs12709735	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12966247	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1866321	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1964984	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2578183	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2578192	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850646	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28524126	0.82[ASN][1000 genomes]
rs35657986	0.82[ASN][1000 genomes]
rs35935345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753069	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4257298	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4275936	0.81[AMR][1000 genomes]
rs4890312	0.86[ASN][1000 genomes]
rs60986007	0.82[ASN][1000 genomes]
rs6507663	0.86[ASN][1000 genomes]
rs6507664	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7238347	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7239525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085233	0.82[ASN][1000 genomes]
rs8096719	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9946831	0.81[ASN][1000 genomes]
rs9950234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954534	0.82[ASN][1000 genomes]
rs9955008	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962297	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9965812	0.81[EUR][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	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3745002	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43650200-43652800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr18:43650800-43652400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr18:43650800-43652400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr18:43650800-43652600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr18:43650800-43652600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr18:43650800-43652600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr18:43650800-43652600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr18:43650800-43652800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr18:43650800-43652800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr18:43650800-43652800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr18:43650800-43653000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr18:43650800-43653000	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr18:43651000-43652400	Active TSS	Brain Anterior Caudate	brain
14	chr18:43651000-43652400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr18:43651000-43652400	Active TSS	HSMM	muscle
16	chr18:43651000-43652600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr18:43651000-43652600	Active TSS	Colon Smooth Muscle	Colon
18	chr18:43651000-43652800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr18:43651000-43652800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr18:43651000-43653000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:43651200-43652400	Active TSS	Brain Cingulate Gyrus	brain
22	chr18:43651200-43652400	Active TSS	Right Atrium	heart
23	chr18:43651200-43652600	Active TSS	Fetal Kidney	kidney
24	chr18:43651200-43652600	Flanking Active TSS	Right Ventricle	heart
25	chr18:43651200-43652600	Active TSS	HSMMtube	muscle
26	chr18:43651200-43652600	Active TSS	NHDF-Ad	bronchial
27	chr18:43651200-43652800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr18:43651200-43652800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr18:43651400-43652400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:43651400-43652400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:43651400-43652400	Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr18:43651400-43652400	Active TSS	Primary T cells from cord blood	blood
33	chr18:43651400-43652400	Active TSS	Psoas Muscle	Psoas
34	chr18:43651400-43652400	Active TSS	Spleen	Spleen
35	chr18:43651400-43652400	Active TSS	NHLF	lung
36	chr18:43651400-43652600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr18:43651400-43652600	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr18:43651400-43652600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr18:43651400-43652600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:43651400-43652600	Active TSS	Aorta	Aorta
41	chr18:43651400-43652600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
42	chr18:43651400-43652600	Active TSS	Gastric	stomach
43	chr18:43651400-43652600	Flanking Active TSS	HUVEC	blood vessel
44	chr18:43651400-43652800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr18:43651400-43652800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr18:43651400-43652800	Active TSS	K562	blood
47	chr18:43651400-43657400	Weak transcription	A549	lung
48	chr18:43651600-43652400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:43651600-43652400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr18:43651600-43652400	Active TSS	Primary monocytes fromperipheralblood	blood

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