Variant report

Variant	rs17670483
Chromosome Location	chr15:40636957-40636958
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	chr15:40636783-40637062	GM10248	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
2	CTCF	chr15:40636840-40636990	HRE	kidney:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
3	EBF1	chr15:40636796-40636999	GM12878	blood:	n/a	chr15:40636891-40636902 chr15:40636891-40636904 chr15:40636837-40636846
4	CTCF	chr15:40636789-40637098	K562	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
5	RAD21	chr15:40636749-40637143	H1-hESC	embryonic stem cell:	n/a	chr15:40636925-40636944
6	SMC3	chr15:40636725-40637160	GM12878	blood:	n/a	n/a
7	CTCF	chr15:40636699-40637260	K562	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
8	STAT1	chr15:40636822-40637043	GM12878	blood:	n/a	n/a
9	CTCF	chr15:40636860-40637010	GM12873	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
10	CTCF	chr15:40636820-40636970	WI-38	lung:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
11	RAD21	chr15:40636757-40637148	GM12878	blood:	n/a	chr15:40636925-40636944
12	CTCF	chr15:40636860-40637010	AG04449	skin:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
13	CTCF	chr15:40636860-40637010	GM12874	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
14	RCOR1	chr15:40636770-40637095	K562	blood:	n/a	n/a
15	CTCF	chr15:40636779-40637158	Pancreas_OC	pancreas:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
16	MAX	chr15:40636811-40637011	K562	blood:	n/a	n/a
17	RAD21	chr15:40636831-40637040	K562	blood:	n/a	chr15:40636925-40636944
18	CTCF	chr15:40636816-40637219	LNCaP	prostate:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
19	CTCF	chr15:40636840-40636990	HEEpiC	esophagus:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
20	MAZ	chr15:40635062-40637277	IMR90	lung:	n/a	n/a
21	CTCF	chr15:40636840-40636990	RPTEC	kidney:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
22	CTCF	chr15:40636840-40636990	HRPEpiC	eye:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
23	BRCA1	chr15:40636882-40637048	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr15:40636514-40637384	A549	lung:	n/a	chr15:40636926-40636947 chr15:40636924-40636942 chr15:40637299-40637312 chr15:40637257-40637266
25	CTCF	chr15:40636860-40637010	AoAF	blood vessel:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
26	CTCF	chr15:40636860-40637010	RPTEC	kidney:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
27	CTCF	chr15:40636789-40637057	Hela-S3	cervix:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
28	CTCF	chr15:40636687-40637101	A549	lung:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
29	CTCF	chr15:40636860-40637010	HA-sp	spinal cord:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
30	CTCF	chr15:40636860-40637010	HEK293	kidney:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
31	CTCF	chr15:40636840-40636990	HFF	foreskin:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
32	CTCF	chr15:40636860-40637010	NHEK	skin:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
33	GTF2F1	chr15:40636839-40637052	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr15:40636840-40636990	HA-sp	spinal cord:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
35	SMC3	chr15:40636629-40637510	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr15:40636880-40637030	GM12864	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
37	RFX5	chr15:40636777-40637083	HepG2	liver:	n/a	n/a
38	RAD21	chr15:40636690-40637199	SK-N-SH_RA	brain:	n/a	chr15:40636925-40636944
39	CTCF	chr15:40636840-40636990	HL-60	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
40	CHD2	chr15:40636815-40637091	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr15:40636783-40637202	MCF-7	breast:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
42	CTCF	chr15:40636860-40637010	HCM	heart:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
43	RAD21	chr15:40636702-40637222	ECC-1	luminal epithelium:	n/a	chr15:40636925-40636944
44	RAD21	chr15:40636609-40637233	IMR90	lung:	n/a	chr15:40636925-40636944
45	SP4	chr15:40636818-40637054	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr15:40636860-40637010	BE2_C	brain:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
47	CTCF	chr15:40636880-40637030	HCFaa	heart:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
48	CTCF	chr15:40636860-40637010	HPAF	blood vessel:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
49	CTCF	chr15:40636796-40637051	GM13976	blood:	n/a	chr15:40636926-40636947 chr15:40636924-40636942
50	CTCF	chr15:40636860-40637010	WI-38	lung:	n/a	chr15:40636926-40636947 chr15:40636924-40636942

No.	Distal block	Cell Line	Cell type
1	chr15:40635356..40637920-chr15:40639112..40641460,3	K562	blood:
2	chr15:40636454..40637675-chr15:40713711..40714788,5	K562	blood:
3	chr15:40636488..40640670-chr15:40658670..40661972,5	MCF-7	breast:
4	chr15:40636483..40637410-chr15:40659872..40660767,3	K562	blood:
5	chr15:40636615..40640420-chr15:40645186..40649108,5	K562	blood:
6	chr15:40635911..40638276-chr15:40731677..40734412,2	K562	blood:
7	chr15:40626473..40628629-chr15:40636681..40638741,2	K562	blood:
8	chr15:40630714..40634859-chr15:40635912..40637951,3	MCF-7	breast:
9	chr15:40636033..40638861-chr15:40659207..40662844,4	K562	blood:
10	chr15:40631655..40634188-chr15:40635440..40637021,2	K562	blood:
11	chr15:40636637..40637408-chr15:40659598..40660412,3	MCF-7	breast:
12	chr15:40636446..40637771-chr15:40659706..40660699,14	MCF-7	breast:
13	chr15:40631754..40634753-chr15:40635668..40637955,3	MCF-7	breast:

Variant related genes	Relation type
C15orf52	TF binding region
ENSG00000140320	Chromatin interaction
ENSG00000140323	Chromatin interaction
ENSG00000259368	Chromatin interaction
ENSG00000188549	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11630891	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634644	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118959	0.81[EUR][1000 genomes]
rs55641696	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62017974	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72731500	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72733403	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
2	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
3	chr15:40629400-40637200	Enhancers	Fetal Lung	lung
4	chr15:40632800-40637000	Weak transcription	Fetal Thymus	thymus
5	chr15:40633000-40637200	Enhancers	Fetal Muscle Leg	muscle
6	chr15:40633000-40637400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:40633000-40637400	Enhancers	NHDF-Ad	bronchial
8	chr15:40633000-40638800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40633000-40640600	Enhancers	Fetal Intestine Small	intestine
10	chr15:40633200-40637400	Enhancers	Right Ventricle	heart
11	chr15:40633200-40637400	Enhancers	HMEC	breast
12	chr15:40633200-40637400	Enhancers	NHEK	skin
13	chr15:40633200-40637400	Enhancers	NHLF	lung
14	chr15:40633200-40637600	Enhancers	HUVEC	blood vessel
15	chr15:40633200-40639400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:40633200-40641600	Enhancers	Esophagus	oesophagus
17	chr15:40633400-40637000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr15:40633400-40637000	Weak transcription	Small Intestine	intestine
19	chr15:40633400-40637200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:40633400-40637800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:40633600-40637200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:40633600-40637200	Enhancers	Osteobl	bone
23	chr15:40633600-40642800	Enhancers	Stomach Mucosa	stomach
24	chr15:40633600-40644800	Weak transcription	Brain Germinal Matrix	brain
25	chr15:40633600-40645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:40633800-40637400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:40633800-40638200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:40633800-40638600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:40633800-40638600	Weak transcription	Hela-S3	cervix
30	chr15:40634000-40638600	Weak transcription	HSMM	muscle
31	chr15:40634200-40637000	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr15:40634200-40637600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:40634400-40637200	Enhancers	NH-A	brain
34	chr15:40634600-40637200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:40634800-40637200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:40634800-40637400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr15:40634800-40641000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr15:40635000-40637200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:40635000-40637400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:40635000-40637400	Enhancers	A549	lung
41	chr15:40635200-40637200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr15:40635200-40637200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:40635200-40637200	Enhancers	Fetal Muscle Trunk	muscle
44	chr15:40635200-40637400	Enhancers	Brain Hippocampus Middle	brain
45	chr15:40635200-40637400	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr15:40635200-40641400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr15:40635400-40637000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:40635600-40637000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:40635600-40637000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:40635600-40637000	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links