Variant report

Variant	rs58856253
Chromosome Location	chr15:75166141-75166142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:65)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:65 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr15:75165095-75166185	SK-N-SH	brain:	n/a	chr15:75165424-75165444
2	TBP	chr15:75165161-75166216	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr15:75165119-75166288	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:75165066-75166210	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr15:75164982-75166402	K562	blood:	n/a	n/a
6	CTCF	chr15:75166040-75166190	GM12866	blood:	n/a	n/a
7	ELF1	chr15:75165033-75166320	MCF-7	breast:	n/a	chr15:75165680-75165691 chr15:75165681-75165690 chr15:75165680-75165691
8	CREB1	chr15:75165213-75166267	A549	lung:	n/a	n/a
9	POLR2A	chr15:75165126-75166324	PFSK-1	brain:	n/a	n/a
10	ZBTB7A	chr15:75165071-75166161	ECC-1	luminal epithelium:	n/a	n/a
11	CREB1	chr15:75165027-75166253	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:75165144-75166371	K562	blood:	n/a	n/a
13	TBL1XR1	chr15:75165391-75166233	K562	blood:	n/a	n/a
14	CTCF	chr15:75166100-75166250	GM12865	blood:	n/a	n/a
15	CTCF	chr15:75166000-75166150	HBMEC	blood vessel:	n/a	n/a
16	MAX	chr15:75165961-75166170	K562	blood:	n/a	n/a
17	NR2F2	chr15:75165203-75166429	K562	blood:	n/a	n/a
18	POLR2A	chr15:75165072-75166213	K562	blood:	n/a	n/a
19	REST	chr15:75164903-75166160	H1-neurons	neurons:	n/a	chr15:75165335-75165345
20	POLR2A	chr15:75164204-75166171	GM12892	blood:	n/a	n/a
21	SIN3AK20	chr15:75164946-75166533	MCF-7	breast:	n/a	n/a
22	MAZ	chr15:75165164-75166218	GM12878	blood:	n/a	n/a
23	KAP1	chr15:75165926-75166290	HEK293	kidney:	n/a	n/a
24	CTCF	chr15:75166080-75166230	HCPEpiC	choroid plexus:	n/a	n/a
25	POLR2A	chr15:75164876-75166315	H1-hESC	embryonic stem cell:	n/a	n/a
26	SIN3A	chr15:75165004-75166344	H1-hESC	embryonic stem cell:	n/a	n/a
27	JUND	chr15:75165294-75166399	K562	blood:	n/a	chr15:75166374-75166383
28	MAZ	chr15:75165197-75166382	K562	blood:	n/a	n/a
29	MAX	chr15:75165082-75166508	A549	lung:	n/a	n/a
30	MAX	chr15:75165202-75166259	GM12878	blood:	n/a	n/a
31	RCOR1	chr15:75166042-75166231	K562	blood:	n/a	n/a
32	MYC	chr15:75166137-75166204	MCF-7	breast:	n/a	n/a
33	MAX	chr15:75165156-75166341	NB4	blood:	n/a	n/a
34	UBTF	chr15:75165921-75166216	K562	blood:	n/a	n/a
35	BHLHE40	chr15:75165955-75166155	K562	blood:	n/a	n/a
36	SMARCB1	chr15:75165153-75166366	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr15:75166040-75166190	GM12873	blood:	n/a	n/a
38	POLR2A	chr15:75164993-75166165	HUVEC	blood vessel:	n/a	n/a
39	MYC	chr15:75165255-75166214	K562	blood:	n/a	n/a
40	MAX	chr15:75165124-75166245	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr15:75165200-75166322	NB4	blood:	n/a	n/a
42	ELF1	chr15:75165007-75166141	HCT-116	colon:	n/a	chr15:75165680-75165691 chr15:75165681-75165690 chr15:75165680-75165691
43	IRF1	chr15:75165223-75166209	K562	blood:	n/a	chr15:75165890-75165904 chr15:75165336-75165350
44	CTCF	chr15:75166100-75166250	AoAF	blood vessel:	n/a	n/a
45	TAF1	chr15:75164982-75166144	ECC-1	luminal epithelium:	n/a	n/a
46	MXI1	chr15:75165113-75166202	HepG2	liver:	n/a	n/a
47	PML	chr15:75164638-75166147	GM12878	blood:	n/a	n/a
48	TBP	chr15:75165098-75166147	K562	blood:	n/a	n/a
49	HCFC1	chr15:75164779-75166171	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr15:75165105-75166255	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75132063..75136088-chr15:75165447..75167881,5	K562	blood:
2	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
3	chr15:75164429..75167842-chr15:75196018..75198435,3	K562	blood:
4	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:
5	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
6	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
7	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
8	chr15:75110223..75112810-chr15:75165268..75167627,2	MCF-7	breast:
9	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
10	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
11	chr15:75164573..75166914-chr15:75228746..75230664,2	K562	blood:

No data

Variant related genes	Relation type
SCAMP2	TF binding region
ENSG00000178761	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000260824	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12101507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12101557	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12439641	0.83[AFR][1000 genomes]
rs12441499	0.87[AFR][1000 genomes]
rs12442804	0.82[AFR][1000 genomes]
rs2230479	0.95[AFR][1000 genomes]
rs28726277	0.82[AFR][1000 genomes]
rs3935818	0.86[AFR][1000 genomes]
rs56671860	0.87[AFR][1000 genomes]
rs60494786	0.87[AFR][1000 genomes]
rs60698434	0.80[AFR][1000 genomes]
rs7179093	0.86[AFR][1000 genomes]
rs729263	0.87[AFR][1000 genomes]
rs8031052	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8032473	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9672491	0.86[AFR][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	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv827386	chr15:75161362-75166473	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
4	nsv827388	chr15:75161362-75169121	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75164200-75166400	Active TSS	Rectal Smooth Muscle	rectum
2	chr15:75164400-75166400	Active TSS	HSMMtube	muscle
3	chr15:75164600-75166200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr15:75164600-75166200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr15:75164600-75166400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:75164600-75166400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr15:75164600-75166400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:75164600-75166400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:75164600-75166400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr15:75164600-75166400	Active TSS	Muscle Satellite Cultured Cells	--
11	chr15:75164600-75166400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:75164600-75166400	Active TSS	Brain Cingulate Gyrus	brain
13	chr15:75164600-75166400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr15:75164600-75166400	Active TSS	A549	lung
15	chr15:75164600-75166600	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr15:75164800-75166200	Active TSS	Aorta	Aorta
17	chr15:75164800-75166200	Active TSS	Esophagus	oesophagus
18	chr15:75164800-75166200	Active TSS	Left Ventricle	heart
19	chr15:75164800-75166200	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr15:75164800-75166400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr15:75164800-75166400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr15:75164800-75166400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr15:75164800-75166400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr15:75164800-75166400	Active TSS	Stomach Mucosa	stomach
25	chr15:75164800-75166400	Active TSS	NHDF-Ad	bronchial
26	chr15:75165000-75166200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:75165000-75166200	Active TSS	Fetal Intestine Small	intestine
28	chr15:75165000-75166200	Active TSS	Psoas Muscle	Psoas
29	chr15:75165000-75166200	Bivalent/Poised TSS	HepG2	liver
30	chr15:75165000-75166400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:75165000-75166400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:75165000-75166400	Active TSS	Brain Anterior Caudate	brain
33	chr15:75165000-75166400	Active TSS	Brain Hippocampus Middle	brain
34	chr15:75165000-75166400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:75165000-75166400	Active TSS	Brain Substantia Nigra	brain
36	chr15:75165000-75166400	Active TSS	Colonic Mucosa	Colon
37	chr15:75165000-75166400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr15:75165000-75166400	Active TSS	Fetal Intestine Large	intestine
39	chr15:75165000-75166400	Active TSS	Fetal Kidney	kidney
40	chr15:75165000-75166400	Active TSS	Pancreas	Pancrea
41	chr15:75165000-75166400	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr15:75165200-75166400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:75165200-75166400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:75165200-75166400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:75165800-75166200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:75165800-75166200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:75165800-75166200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr15:75165800-75166200	Flanking Active TSS	Fetal Lung	lung
49	chr15:75165800-75166200	Active TSS	Right Atrium	heart
50	chr15:75165800-75166200	Flanking Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links