Variant report

Variant	rs13182141
Chromosome Location	chr5:179126632-179126633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:189)
CpG islands
(count:0)
Chromatin interactive
region (count:44)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:189 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179124743-179127945	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:179124762-179127291	U87	brain:	n/a	n/a
3	TBL1XR1	chr5:179124963-179126913	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:179124942-179127184	GM18951	blood:	n/a	n/a
5	MXI1	chr5:179125029-179127865	K562	blood:	n/a	n/a
6	JUND	chr5:179125184-179126821	K562	blood:	n/a	n/a
7	POLR2A	chr5:179124985-179127227	GM19193	blood:	n/a	n/a
8	BCL11A	chr5:179126564-179126938	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:179124912-179127286	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:179124768-179127291	U87	brain:	n/a	n/a
11	TAL1	chr5:179125911-179127898	K562	blood:	n/a	n/a
12	ZMIZ1	chr5:179125009-179127175	K562	blood:	n/a	n/a
13	PML	chr5:179124897-179127985	K562	blood:	n/a	n/a
14	ATF2	chr5:179126467-179127325	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:179126500-179127917	K562	blood:	n/a	n/a
16	SP1	chr5:179124948-179126936	HCT-116	colon:	n/a	chr5:179125874-179125888 chr5:179125681-179125690 chr5:179126320-179126330 chr5:179125877-179125889 chr5:179125681-179125690 chr5:179125680-179125692 chr5:179125724-179125735 chr5:179125682-179125691 chr5:179125680-179125692 chr5:179125725-179125734
17	MAX	chr5:179125082-179127020	MCF-7	breast:	n/a	chr5:179125996-179126005
18	HCFC1	chr5:179125078-179127269	K562	blood:	n/a	n/a
19	MXI1	chr5:179124915-179127297	GM12878	blood:	n/a	n/a
20	NFIC	chr5:179126398-179127143	GM12878	blood:	n/a	n/a
21	TBP	chr5:179126525-179127633	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:179126605-179126920	HepG2	liver:	n/a	n/a
23	POLR2A	chr5:179124931-179127807	PBDE	blood:	n/a	n/a
24	BATF	chr5:179126536-179126983	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:179126447-179127870	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:179124705-179127154	PFSK-1	brain:	n/a	n/a
27	HDAC2	chr5:179126596-179126969	HepG2	liver:	n/a	n/a
28	BATF	chr5:179126595-179126928	GM12878	blood:	n/a	n/a
29	PML	chr5:179124829-179127939	K562	blood:	n/a	n/a
30	POLR2A	chr5:179124857-179127272	GM18505	blood:	n/a	n/a
31	POLR2A	chr5:179125133-179127239	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:179126608-179126949	ECC-1	luminal epithelium:	n/a	n/a
33	NR2F2	chr5:179124886-179127970	K562	blood:	n/a	chr5:179126348-179126363
34	POLR2A	chr5:179125764-179127290	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr5:179124836-179126974	PANC-1	pancreas:	n/a	n/a
36	MXI1	chr5:179125044-179126893	Hela-S3	cervix:	n/a	n/a
37	MYC	chr5:179125221-179126766	MCF10A-Er-Src	breast:	n/a	chr5:179125996-179126005
38	TAF1	chr5:179126454-179126885	GM12878	blood:	n/a	n/a
39	REST	chr5:179124809-179127096	H1-neurons	neurons:	n/a	chr5:179126419-179126432
40	HEY1	chr5:179125142-179127248	HepG2	liver:	n/a	chr5:179125960-179125975
41	POLR2A	chr5:179126360-179126985	ECC-1	luminal epithelium:	n/a	n/a
42	MXI1	chr5:179124817-179127952	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr5:179124995-179127254	GM12892	blood:	n/a	n/a
44	MAX	chr5:179126608-179127182	K562	blood:	n/a	n/a
45	SIN3AK20	chr5:179126525-179126927	A549	lung:	n/a	n/a
46	POLR2A	chr5:179124787-179127911	K562	blood:	n/a	n/a
47	POLR2A	chr5:179124888-179127798	GM19099	blood:	n/a	n/a
48	PML	chr5:179124785-179127152	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:179124706-179127975	GM12892	blood:	n/a	n/a
50	POLR2A	chr5:179125141-179127190	Hela-S3	cervix:	n/a	n/a

No data

(count:44 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179125105..179126720-chr5:179232704..179234457,2	MCF-7	breast:
2	chr5:179123586..179129079-chr5:179129217..179136579,19	MCF-7	breast:
3	chr5:179123960..179129281-chr5:179231995..179235216,8	K562	blood:
4	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
5	chr5:179125663..179128297-chr5:179149056..179150816,2	MCF-7	breast:
6	chr5:172753236..172756194-chr5:179125387..179127082,2	MCF-7	breast:
7	chr5:178998693..179001088-chr5:179125400..179127599,2	K562	blood:
8	chr5:179125392..179128992-chr5:179244423..179246560,4	K562	blood:
9	chr5:179123960..179129252-chr5:179231413..179236095,7	K562	blood:
10	chr5:179034167..179038139-chr5:179125249..179127406,3	MCF-7	breast:
11	chr12:131354751..131357004-chr5:179125942..179127682,2	MCF-7	breast:
12	chr5:179040431..179043437-chr5:179125236..179127869,3	K562	blood:
13	chr5:179122850..179128148-chr5:179246584..179249342,5	K562	blood:
14	chr5:179047558..179053114-chr5:179123905..179129187,22	K562	blood:
15	chr10:75936117..75936713-chr5:179125923..179126832,2	NB4	blood:
16	chr5:178985235..178987908-chr5:179124412..179127341,2	MCF-7	breast:
17	chr5:179126146..179127712-chr5:179333460..179335651,2	MCF-7	breast:
18	chr5:179123896..179127851-chr5:179243560..179246560,5	K562	blood:
19	chr5:178976329..178981059-chr5:179123787..179127407,6	K562	blood:
20	chr5:179124990..179127718-chr5:179220717..179222385,2	K562	blood:
21	chr5:179126009..179127718-chr5:179220885..179222493,2	K562	blood:
22	chr5:179124684..179126939-chr5:179285490..179289046,3	MCF-7	breast:
23	chr5:179123572..179126776-chr5:179221240..179224069,3	MCF-7	breast:
24	chr5:179126083..179129267-chr5:179148624..179150852,3	K562	blood:
25	chr5:178976850..178979581-chr5:179125172..179127163,2	K562	blood:
26	chr5:179124597..179127055-chr5:179246139..179249577,4	MCF-7	breast:
27	chr5:179049208..179051645-chr5:179125705..179129690,6	MCF-7	breast:
28	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
29	chr5:179125840..179127525-chr5:179233336..179235588,2	MCF-7	breast:
30	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
31	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
32	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
33	chr5:179124982..179127073-chr5:179245665..179248620,3	MCF-7	breast:
34	chr3:57261301..57262192-chr5:179126361..179126871,2	Hela-S3	cervix:
35	chr5:179121400..179128828-chr5:179157984..179161377,21	K562	blood:
36	chr1:28975008..28975511-chr5:179126447..179127179,2	Hela-S3	cervix:
37	chr5:179123632..179128657-chr5:179156913..179163491,14	MCF-7	breast:
38	chr5:179124533..179126912-chr5:179247842..179250922,3	K562	blood:
39	chr5:179124035..179127505-chr5:179157238..179162405,12	MCF-7	breast:
40	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:
41	chr5:179049048..179052854-chr5:179122221..179127718,16	MCF-7	breast:
42	chr5:179123773..179127716-chr5:179220848..179225521,8	MCF-7	breast:
43	chr5:179125142..179127664-chr5:179134818..179137175,2	MCF-7	breast:
44	chr5:179125163..179127622-chr5:179228110..179231035,2	K562	blood:

No data

Variant related genes	Relation type
CANX	TF binding region
ENSG00000197226	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000156110	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000157500	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000249140	Chromatin interaction
ENSG00000221394	Chromatin interaction
ENSG00000204659	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000132341	Chromatin interaction
ENSG00000113739	Chromatin interaction
ENSG00000161021	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1019443	0.86[JPT][hapmap]
rs10516146	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs10903245	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11744662	0.84[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12374446	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12374485	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12518476	0.81[LWK][hapmap];0.84[YRI][hapmap]
rs12522926	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap]
rs12652934	0.86[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap]
rs13164674	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13174472	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34329357	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34646062	0.92[YRI][hapmap]
rs35320050	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3797774	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs6601073	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs7732112	0.83[AFR][1000 genomes]
rs7736300	0.81[CEU][hapmap];0.86[JPT][hapmap]

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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13182141	C5orf45	cis	cerebellum	SCAN
rs13182141	TSPAN17	cis	cerebellum	SCAN
rs13182141	CANX	cis	parietal	SCAN
rs13182141	HRH2	cis	parietal	SCAN
rs13182141	HNRNPH1	cis	parietal	SCAN
rs13182141	MAML1	cis	lymphoblastoid	seeQTL
rs13182141	CANX	cis	cerebellum	SCAN
rs13182141	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179124200-179127800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:179124400-179127800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:179124600-179126800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:179124600-179127400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:179124600-179127600	Active TSS	HSMM	muscle
6	chr5:179124800-179127000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:179124800-179127000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:179124800-179127000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr5:179124800-179127000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:179124800-179127200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:179124800-179127400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr5:179124800-179127400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:179124800-179127400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:179124800-179127400	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:179124800-179127400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr5:179124800-179127400	Active TSS	Psoas Muscle	Psoas
17	chr5:179124800-179127400	Active TSS	NHEK	skin
18	chr5:179124800-179127600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:179124800-179127600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:179124800-179127600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:179124800-179127800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:179125000-179126800	Active TSS	Fetal Lung	lung
23	chr5:179125000-179127000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:179125000-179127000	Active TSS	Brain Hippocampus Middle	brain
25	chr5:179125000-179127000	Active TSS	Small Intestine	intestine
26	chr5:179125000-179127200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:179125000-179127200	Active TSS	Esophagus	oesophagus
28	chr5:179125000-179127200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr5:179125000-179127200	Bivalent/Poised TSS	HepG2	liver
30	chr5:179125000-179127400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr5:179125000-179127400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:179125000-179127400	Active TSS	Aorta	Aorta
33	chr5:179125000-179127400	Active TSS	Left Ventricle	heart
34	chr5:179125000-179127400	Active TSS	Right Ventricle	heart
35	chr5:179125000-179127400	Active TSS	Osteobl	bone
36	chr5:179125000-179127600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr5:179125000-179127600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:179125000-179127600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:179125000-179127600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:179125000-179127600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:179125000-179127600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr5:179125000-179127600	Active TSS	Fetal Muscle Trunk	muscle
43	chr5:179125000-179127600	Active TSS	Lung	lung
44	chr5:179125000-179127600	Active TSS	Ovary	ovary
45	chr5:179125200-179126800	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr5:179125200-179126800	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr5:179125200-179126800	Active TSS	Brain Cingulate Gyrus	brain
48	chr5:179125200-179126800	Active TSS	Stomach Smooth Muscle	stomach
49	chr5:179125200-179126800	Active TSS	Hela-S3	cervix
50	chr5:179125200-179127000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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