Variant report

Variant	rs72733403
Chromosome Location	chr15:40630913-40630914
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	POLR2A	chr15:40630789-40633526	U87	brain:	n/a	n/a
2	MAZ	chr15:40629940-40633888	IMR90	lung:	n/a	chr15:40632042-40632058
3	CTCF	chr15:40630858-40630962	GM12891	blood:	n/a	n/a
4	EP300	chr15:40630746-40631940	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr15:40630743-40631785	ECC-1	luminal epithelium:	n/a	n/a
6	FOSL2	chr15:40630663-40631676	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr15:40630840-40630990	SAEC	small airway:	n/a	n/a
8	CTCF	chr15:40629943-40631259	SK-N-SH	brain:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
9	CTCF	chr15:40630820-40630970	HCM	heart:	n/a	n/a
10	POLR2A	chr15:40630881-40633380	U87	brain:	n/a	n/a
11	CTCF	chr15:40630853-40630937	GM19239	blood:	n/a	n/a
12	CTCF	chr15:40630257-40630917	GM12892	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
13	POLR2A	chr15:40630212-40633443	IMR90	lung:	n/a	n/a
14	POLR2A	chr15:40630797-40631524	ProgFib	skin:	n/a	n/a
15	POLR2A	chr15:40630776-40633457	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr15:40630896-40633380	U87	brain:	n/a	n/a
17	CTCF	chr15:40630258-40631079	GM19238	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
18	ZBTB7A	chr15:40630170-40631708	ECC-1	luminal epithelium:	n/a	n/a
19	TEAD4	chr15:40630887-40631777	SK-N-SH	brain:	n/a	n/a
20	ZBTB7A	chr15:40630110-40633237	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:40630215-40633532	U87	brain:	n/a	n/a
22	CTCF	chr15:40630820-40630970	GM12875	blood:	n/a	n/a
23	TCF12	chr15:40630913-40631780	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr15:40630907-40631622	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr15:40630162-40633385	PANC-1	pancreas:	n/a	n/a
26	NFIC	chr15:40630876-40631750	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr15:40630911-40630930	GM19240	blood:	n/a	n/a
28	CTCF	chr15:40630900-40631050	GM12866	blood:	n/a	n/a
29	CTCF	chr15:40629925-40631112	A549	lung:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
30	CTCF	chr15:40630883-40630985	NHEK	skin:	n/a	n/a
31	MAX	chr15:40630182-40631577	A549	lung:	n/a	n/a
32	TEAD4	chr15:40630827-40631639	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr15:40630896-40633272	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40628035..40631006-chr15:40631506..40634762,3	MCF-7	breast:
2	chr15:40583247..40584804-chr15:40630582..40632469,2	MCF-7	breast:
3	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
4	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:

Variant related genes	Relation type
C15orf52	TF binding region
ENSG00000188549	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11630891	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11634644	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670483	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118959	0.89[EUR][1000 genomes]
rs28602975	0.88[EUR][1000 genomes]
rs55641696	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62017974	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72731500	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
2	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
3	chr15:40622400-40633800	Enhancers	Spleen	Spleen
4	chr15:40625800-40631600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
6	chr15:40626400-40631600	Enhancers	Adipose Nuclei	Adipose
7	chr15:40626600-40631800	Enhancers	Duodenum Mucosa	Duodenum
8	chr15:40626600-40633800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:40627000-40632200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr15:40627000-40633400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:40627600-40631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:40627800-40632200	Weak transcription	Small Intestine	intestine
13	chr15:40628000-40631200	Genic enhancers	Esophagus	oesophagus
14	chr15:40628600-40631000	Transcr. at gene 5' and 3'	HMEC	breast
15	chr15:40628800-40633600	Enhancers	Placenta	Placenta
16	chr15:40629000-40632000	Enhancers	Fetal Muscle Trunk	muscle
17	chr15:40629000-40632400	Enhancers	Fetal Intestine Small	intestine
18	chr15:40629200-40631200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
19	chr15:40629400-40631000	Enhancers	Left Ventricle	heart
20	chr15:40629400-40631600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:40629400-40633600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:40629400-40637200	Enhancers	Fetal Lung	lung
23	chr15:40629600-40632000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:40629600-40632000	Enhancers	Fetal Muscle Leg	muscle
25	chr15:40629600-40633400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:40629600-40633600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:40629600-40633600	Enhancers	Ovary	ovary
28	chr15:40629800-40631200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:40629800-40631400	Enhancers	Psoas Muscle	Psoas
30	chr15:40629800-40631400	Enhancers	HUVEC	blood vessel
31	chr15:40629800-40631600	Transcr. at gene 5' and 3'	NHEK	skin
32	chr15:40629800-40631800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:40629800-40631800	Flanking Active TSS	HSMM	muscle
34	chr15:40629800-40632000	Enhancers	Brain Germinal Matrix	brain
35	chr15:40629800-40632600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:40629800-40633600	Flanking Active TSS	Colonic Mucosa	Colon
37	chr15:40629800-40634000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr15:40630000-40631000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:40630000-40632200	Enhancers	Fetal Stomach	stomach
40	chr15:40630000-40632200	Enhancers	Stomach Mucosa	stomach
41	chr15:40630000-40632600	Flanking Active TSS	HSMMtube	muscle
42	chr15:40630000-40633400	Enhancers	Fetal Brain Male	brain
43	chr15:40630000-40633400	Flanking Active TSS	NH-A	brain
44	chr15:40630000-40633600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:40630000-40633600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr15:40630200-40631200	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr15:40630200-40631200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr15:40630200-40631400	Enhancers	HepG2	liver
49	chr15:40630200-40632400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr15:40630200-40633000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links