Variant report

Variant	rs7239525
Chromosome Location	chr18:43654033-43654034
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	CTCF	chr18:43653782-43654071	MCF-7	breast:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
2	RAD21	chr18:43653664-43654089	SK-N-SH_RA	brain:	n/a	chr18:43653889-43653908
3	RAD21	chr18:43653585-43654152	ECC-1	luminal epithelium:	n/a	chr18:43653889-43653908
4	MAX	chr18:43653802-43654044	NB4	blood:	n/a	n/a
5	CTCF	chr18:43653742-43654041	A549	lung:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
6	CTCF	chr18:43653764-43654054	HUVEC	blood vessel:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
7	RAD21	chr18:43653505-43654171	HCT-116	colon:	n/a	chr18:43653889-43653908
8	CTCF	chr18:43653028-43654282	SK-N-SH	brain:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
9	RAD21	chr18:43653667-43654053	GM12878	blood:	n/a	chr18:43653889-43653908
10	RAD21	chr18:43653757-43654095	GM12878	blood:	n/a	chr18:43653889-43653908
11	CTCF	chr18:43653714-43654050	SK-N-SH_RA	brain:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
12	RAD21	chr18:43653626-43654171	A549	lung:	n/a	chr18:43653889-43653908
13	SMC3	chr18:43653674-43654102	HepG2	liver:	n/a	chr18:43653893-43653907
14	CTCF	chr18:43653493-43654260	HCT-116	colon:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
15	CTCF	chr18:43653805-43654069	K562	blood:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
16	CTCF	chr18:43653748-43654046	Lung_OC	lung:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
17	ARID3A	chr18:43653670-43654113	HepG2	liver:	n/a	n/a
18	RAD21	chr18:43653694-43654104	HepG2	liver:	n/a	chr18:43653889-43653908
19	FOS	chr18:43653746-43654124	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr18:43653596-43654074	GM12878	blood:	n/a	chr18:43653889-43653908
21	RAD21	chr18:43653350-43654199	ECC-1	luminal epithelium:	n/a	chr18:43653889-43653908
22	CTCF	chr18:43653676-43654159	MCF-7	breast:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
23	CTCF	chr18:43653311-43654265	A549	lung:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
24	MYC	chr18:43653683-43654086	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr18:43653639-43654126	HepG2	liver:	n/a	n/a
26	RAD21	chr18:43653519-43654088	Hela-S3	cervix:	n/a	chr18:43653889-43653908
27	POLR2A	chr18:43653769-43654221	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr18:43653812-43654035	GM10248	blood:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
29	CTCF	chr18:43653789-43654034	T-47D	breast:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
30	RAD21	chr18:43653495-43654119	SK-N-SH_RA	brain:	n/a	chr18:43653889-43653908
31	RAD21	chr18:43653480-43654108	H1-hESC	embryonic stem cell:	n/a	chr18:43653889-43653908
32	RAD21	chr18:43653640-43654076	K562	blood:	n/a	chr18:43653889-43653908
33	SMC3	chr18:43653141-43654309	SK-N-SH	brain:	n/a	chr18:43653893-43653907
34	SMC3	chr18:43653703-43654049	K562	blood:	n/a	chr18:43653893-43653907
35	CTCF	chr18:43653777-43654037	GM12878	blood:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
36	CTCF	chr18:43653782-43654039	LNCaP	prostate:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
37	POLR2A	chr18:43653747-43654152	K562	blood:	n/a	n/a
38	RAD21	chr18:43653617-43654167	HepG2	liver:	n/a	chr18:43653889-43653908
39	TBL1XR1	chr18:43653691-43654066	K562	blood:	n/a	n/a
40	RAD21	chr18:43653613-43654150	MCF-7	breast:	n/a	chr18:43653889-43653908
41	POLR2A	chr18:43653764-43654073	SK-N-SH	brain:	n/a	n/a
42	JUND	chr18:43653782-43654058	K562	blood:	n/a	n/a
43	POLR2A	chr18:43653988-43654089	GM12878	blood:	n/a	n/a
44	CTCF	chr18:43653599-43654115	K562	blood:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
45	FOS	chr18:43653816-43654059	MCF10A-Er-Src	breast:	n/a	n/a
46	RAD21	chr18:43653162-43654276	SK-N-SH	brain:	n/a	chr18:43653889-43653908
47	SMC3	chr18:43653661-43654131	GM12878	blood:	n/a	chr18:43653893-43653907
48	MAZ	chr18:43653740-43654076	GM12878	blood:	n/a	n/a
49	CTCF	chr18:43653715-43654128	A549	lung:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
50	CTCF	chr18:43653790-43654034	Medullo	brain:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908

No.	Distal block	Cell Line	Cell type
1	chr18:43553826..43554616-chr18:43653485..43654035,3	MCF-7	breast:
2	chr18:43653881..43655599-chr18:43657132..43659332,2	K562	blood:
3	chr18:43553938..43554665-chr18:43653434..43654381,2	MCF-7	breast:
4	chr18:43244763..43245742-chr18:43653653..43654356,2	MCF-7	breast:

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	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12966247	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1866321	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1964984	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2578183	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2578192	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850646	0.85[AFR][1000 genomes];0.97[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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745002	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753069	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4257298	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4275936	0.82[AMR][1000 genomes]
rs4890312	0.86[ASN][1000 genomes]
rs60986007	0.82[ASN][1000 genomes]
rs6507663	0.86[ASN][1000 genomes]
rs6507664	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7238347	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8085233	0.82[ASN][1000 genomes]
rs8096719	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9946831	0.81[ASN][1000 genomes]
rs9950234	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954534	0.82[ASN][1000 genomes]
rs9955008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962297	0.89[AFR][1000 genomes];0.84[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
rs7239525	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	chr18:43651400-43657400	Weak transcription	A549	lung
2	chr18:43651600-43657600	Weak transcription	Dnd41	blood
3	chr18:43652200-43659600	Weak transcription	Small Intestine	intestine
4	chr18:43652600-43654200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr18:43652600-43654200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr18:43652600-43654200	Enhancers	HMEC	breast
7	chr18:43652600-43656800	Weak transcription	NHEK	skin
8	chr18:43652600-43657000	Weak transcription	GM12878-XiMat	blood
9	chr18:43652600-43657400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:43652600-43657400	Weak transcription	Brain Anterior Caudate	brain
11	chr18:43652600-43657400	Weak transcription	Thymus	Thymus
12	chr18:43652600-43657400	Weak transcription	HSMMtube	muscle
13	chr18:43652600-43657600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:43652600-43657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr18:43652600-43657600	Weak transcription	Brain Substantia Nigra	brain
16	chr18:43652600-43657600	Weak transcription	Right Atrium	heart
17	chr18:43652600-43657600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr18:43652600-43657800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:43652600-43660000	Weak transcription	Brain Angular Gyrus	brain
20	chr18:43652600-43662200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr18:43652600-43662600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr18:43652600-43663000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:43652600-43663200	Weak transcription	Esophagus	oesophagus
24	chr18:43652600-43665000	Weak transcription	Aorta	Aorta
25	chr18:43652800-43654200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr18:43652800-43654200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr18:43652800-43654200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr18:43652800-43654200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr18:43652800-43654200	Enhancers	NHLF	lung
30	chr18:43652800-43654200	Enhancers	Osteobl	bone
31	chr18:43652800-43654600	Enhancers	Liver	Liver
32	chr18:43652800-43656200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr18:43652800-43657200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr18:43652800-43657400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:43652800-43657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr18:43652800-43657400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr18:43652800-43657600	Weak transcription	Brain Hippocampus Middle	brain
38	chr18:43652800-43657800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:43652800-43659000	Weak transcription	HUVEC	blood vessel
40	chr18:43652800-43659400	Weak transcription	Hela-S3	cervix
41	chr18:43652800-43662600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr18:43652800-43664000	Weak transcription	K562	blood
43	chr18:43653000-43654200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr18:43653000-43654200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr18:43653000-43656800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr18:43653000-43657400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr18:43653000-43657400	Weak transcription	Placenta	Placenta
48	chr18:43653000-43657600	Weak transcription	Fetal Intestine Small	intestine
49	chr18:43653000-43658800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr18:43653000-43659000	Weak transcription	Fetal Intestine Large	intestine

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