Variant report

Variant	rs8041445
Chromosome Location	chr15:40630372-40630373
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	CTCF	chr15:40630340-40630490	SK-N-SH_RA	brain:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
2	RAD21	chr15:40630296-40630566	K562	blood:	n/a	chr15:40630419-40630438
3	MAZ	chr15:40629940-40633888	IMR90	lung:	n/a	chr15:40632042-40632058
4	RAD21	chr15:40630204-40630662	ECC-1	luminal epithelium:	n/a	chr15:40630419-40630438
5	RAD21	chr15:40630258-40630595	GM12878	blood:	n/a	chr15:40630419-40630438
6	CTCF	chr15:40630290-40630613	MCF-7	breast:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
7	CTCF	chr15:40630360-40630510	GM12866	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
8	RAD21	chr15:40630256-40630573	K562	blood:	n/a	chr15:40630419-40630438
9	CTCF	chr15:40630360-40630510	Hela-S3	cervix:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
10	MYC	chr15:40630248-40630616	K562	blood:	n/a	n/a
11	CTCF	chr15:40630360-40630510	BJ	skin:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
12	CTCF	chr15:40630360-40630510	GM12868	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
13	RAD21	chr15:40630192-40630592	HepG2	liver:	n/a	chr15:40630419-40630438
14	ZBTB7A	chr15:40630316-40630601	HepG2	liver:	n/a	n/a
15	CTCF	chr15:40630232-40630797	Spleen_OC	spleen:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
16	CTCF	chr15:40630340-40630490	HEK293	kidney:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
17	ZC3H11A	chr15:40630269-40630565	K562	blood:	n/a	n/a
18	MAX	chr15:40630213-40630590	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr15:40630297-40630513	SK-N-SH_RA	brain:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
20	CTCF	chr15:40629943-40631259	SK-N-SH	brain:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
21	CTCF	chr15:40630332-40630506	A549	lung:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
22	RCOR1	chr15:40630195-40630479	K562	blood:	n/a	n/a
23	RAD21	chr15:40630160-40630586	HepG2	liver:	n/a	chr15:40630419-40630438
24	CTCF	chr15:40630251-40630509	A549	lung:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
25	CTCF	chr15:40630307-40630584	Kidney_OC	kidney:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
26	MAX	chr15:40630189-40630602	NB4	blood:	n/a	n/a
27	FOXA2	chr15:40630341-40630532	HepG2	liver:	n/a	n/a
28	CTCF	chr15:40630225-40630553	T-47D	breast:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
29	GTF2F1	chr15:40630357-40630468	K562	blood:	n/a	n/a
30	SP1	chr15:40630245-40630591	GM12878	blood:	n/a	chr15:40630516-40630525 chr15:40630469-40630483 chr15:40630518-40630532
31	CTCF	chr15:40630360-40630510	GM12867	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
32	CTCF	chr15:40630266-40630628	K562	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
33	CTCF	chr15:40630360-40630510	HCT-116	colon:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
34	JUND	chr15:40630221-40630625	K562	blood:	n/a	n/a
35	MAZ	chr15:40630197-40630777	K562	blood:	n/a	n/a
36	CREB1	chr15:40630265-40630516	A549	lung:	n/a	n/a
37	RAD21	chr15:40630142-40630675	H1-hESC	embryonic stem cell:	n/a	chr15:40630419-40630438
38	CTCF	chr15:40630340-40630490	NHLF	lung:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
39	CTCF	chr15:40630244-40630582	HepG2	liver:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
40	CTCF	chr15:40630320-40630470	GM12869	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
41	CTCF	chr15:40630269-40630816	GM12891	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
42	FOXP2	chr15:40630203-40630552	SK-N-MC	brain:	n/a	n/a
43	CTCF	chr15:40630329-40630574	GM13976	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
44	POLR2A	chr15:40630272-40630678	U87	brain:	n/a	n/a
45	POLR2A	chr15:40630262-40630771	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr15:40630360-40630510	HCM	heart:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
47	CTCF	chr15:40630360-40630510	HBMEC	blood vessel:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
48	CTCF	chr15:40630303-40630578	MCF-7	breast:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
49	SP4	chr15:40630171-40630580	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr15:40630360-40630510	GM12871	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439

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

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

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs55904487	1.00[AMR][1000 genomes]
rs57094441	1.00[AMR][1000 genomes]
rs59636068	1.00[AMR][1000 genomes]
rs60397708	1.00[AMR][1000 genomes]
rs7164303	1.00[AMR][1000 genomes]
rs74011146	1.00[AMR][1000 genomes]
rs74011152	1.00[AMR][1000 genomes]
rs74011153	1.00[AMR][1000 genomes]
rs74013054	1.00[AMR][1000 genomes]
rs74013056	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040294	1.00[AMR][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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
2	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
3	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
4	chr15:40622400-40633800	Enhancers	Spleen	Spleen
5	chr15:40623000-40630600	Weak transcription	Aorta	Aorta
6	chr15:40623800-40630600	Enhancers	Fetal Thymus	thymus
7	chr15:40624200-40630400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:40624200-40630600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:40625800-40630400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:40625800-40630600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr15:40625800-40630600	Enhancers	NHDF-Ad	bronchial
12	chr15:40625800-40631600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
14	chr15:40626400-40630400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:40626400-40631600	Enhancers	Adipose Nuclei	Adipose
16	chr15:40626600-40631800	Enhancers	Duodenum Mucosa	Duodenum
17	chr15:40626600-40633800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:40627000-40630400	Weak transcription	Fetal Brain Female	brain
19	chr15:40627000-40630800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:40627000-40632200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:40627000-40633400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:40627400-40630400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
23	chr15:40627400-40630600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr15:40627400-40630600	Weak transcription	Liver	Liver
25	chr15:40627600-40631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:40627800-40632200	Weak transcription	Small Intestine	intestine
27	chr15:40628000-40631200	Genic enhancers	Esophagus	oesophagus
28	chr15:40628600-40631000	Transcr. at gene 5' and 3'	HMEC	breast
29	chr15:40628800-40630600	Enhancers	Primary B cells from peripheral blood	blood
30	chr15:40628800-40633600	Enhancers	Placenta	Placenta
31	chr15:40629000-40630800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:40629000-40632000	Enhancers	Fetal Muscle Trunk	muscle
33	chr15:40629000-40632400	Enhancers	Fetal Intestine Small	intestine
34	chr15:40629200-40630400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:40629200-40630800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr15:40629200-40631200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
37	chr15:40629400-40630600	Enhancers	Brain Substantia Nigra	brain
38	chr15:40629400-40631000	Enhancers	Left Ventricle	heart
39	chr15:40629400-40631600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:40629400-40633600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:40629400-40637200	Enhancers	Fetal Lung	lung
42	chr15:40629600-40630600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:40629600-40630600	Weak transcription	Gastric	stomach
44	chr15:40629600-40630600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr15:40629600-40632000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr15:40629600-40632000	Enhancers	Fetal Muscle Leg	muscle
47	chr15:40629600-40633400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:40629600-40633600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:40629600-40633600	Enhancers	Ovary	ovary
50	chr15:40629800-40630400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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