Variant report

Variant	rs541641952
Chromosome Location	chr15:45479766-45479767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr15:45479617-45480332	GM12878	blood:	n/a	chr15:45480235-45480250 chr15:45480236-45480249 chr15:45479955-45479969 chr15:45480241-45480251 chr15:45480238-45480248 chr15:45480236-45480249 chr15:45480022-45480032 chr15:45480021-45480031
2	EGR1	chr15:45479644-45480173	K562	blood:	n/a	chr15:45479955-45479969 chr15:45480022-45480032 chr15:45480021-45480031
3	POLR2A	chr15:45478871-45480608	HepG2	liver:	n/a	n/a
4	MAZ	chr15:45479023-45481127	IMR90	lung:	n/a	chr15:45480427-45480434 chr15:45480239-45480249 chr15:45480425-45480434
5	CTCF	chr15:45479680-45479830	BJ	skin:	n/a	n/a
6	ZBTB7A	chr15:45479081-45480112	ECC-1	luminal epithelium:	n/a	n/a
7	ZBTB7A	chr15:45479738-45479906	HepG2	liver:	n/a	n/a
8	REST	chr15:45478783-45481200	H1-neurons	neurons:	n/a	n/a
9	MXI1	chr15:45476431-45481208	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr15:45479760-45479910	GM12867	blood:	n/a	n/a
11	CTCF	chr15:45479720-45479870	HUVEC	blood vessel:	n/a	n/a
12	ZBTB7A	chr15:45479612-45480167	K562	blood:	n/a	n/a
13	ZBTB7A	chr15:45479524-45480181	K562	blood:	n/a	n/a
14	CTCF	chr15:45479660-45479810	GM12870	blood:	n/a	n/a
15	CTCF	chr15:45479760-45479910	GM12869	blood:	n/a	n/a
16	SIN3A	chr15:45479009-45479769	H1-hESC	embryonic stem cell:	n/a	chr15:45479136-45479145
17	CTCF	chr15:45479760-45479910	GM12868	blood:	n/a	n/a
18	ZBTB7A	chr15:45479478-45480237	ECC-1	luminal epithelium:	n/a	n/a
19	EGR1	chr15:45479596-45480191	K562	blood:	n/a	chr15:45479955-45479969 chr15:45480022-45480032 chr15:45480021-45480031

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:45479755-45479805	Caco-2	colon:	n/a
2	chr15:45479755-45479805	SK-N-SH	brain:	n/a
3	chr15:45479755-45479805	HRE	kidney:	n/a
4	chr15:45479755-45479805	BE2_C	brain:	n/a
5	chr15:45479755-45479805	HEEpiC	esophagus:	n/a
6	chr15:45479755-45479805	NH-A	brain:	n/a
7	chr15:45479755-45479805	SAEC	small airway:	n/a
8	chr15:45479755-45479805	AoSMC	blood vessel:	n/a
9	chr15:45479755-45479805	ProgFib	skin:	n/a
10	chr15:45479755-45479805	IMR90	lung:	fetal
11	chr15:45479755-45479805	HL-60	blood:	n/a
12	chr15:45479755-45479805	MCF-7	breast:	n/a
13	chr15:45479755-45479805	NHDF-neo	bronchial:	n/a
14	chr15:45479755-45479805	HUVEC	blood vessel:	n/a
15	chr15:45479755-45479805	RPTEC	kidney:	n/a
16	chr15:45479755-45479805	HCPEpiC	choroid plexus:	n/a
17	chr15:45479755-45479805	AG04449	skin:	fetal
18	chr15:45479755-45479805	U87	brain:	n/a
19	chr15:45479755-45479805	Jurkat	blood:	n/a
20	chr15:45479755-45479805	Hepatocyte	liver:	n/a
21	chr15:45479755-45479805	HAEpiC	amniotic membrane:	n/a
22	chr15:45479755-45479805	HRPEpiC	eye:	n/a
23	chr15:45479755-45479805	ovcar-3	ovarian:	n/a
24	chr15:45479755-45479805	K562	blood:	n/a
25	chr15:45479755-45479805	ECC-1	luminal epithelium:	n/a
26	chr15:45479755-45479805	PrEC	prostate:	n/a
27	chr15:45479755-45479805	Hela-S3	cervix:	n/a
28	chr15:45479755-45479805	GM19239	blood:	n/a
29	chr15:45479755-45479805	NHBE	bronchial:	n/a
30	chr15:45479755-45479805	SK-N-SH_RA	brain:	n/a
31	chr15:45479755-45479805	HCM	heart:	n/a
32	chr15:45479755-45479805	HMEC	breast:	n/a
33	chr15:45479755-45479805	BJ	skin:	n/a
34	chr15:45479755-45479805	GM06990	blood:	n/a
35	chr15:45479755-45479805	HPAEpiC	pulmonary alveolar:	n/a
36	chr15:45479755-45479805	HEK293	kidney:	embryo
37	chr15:45479755-45479805	MCF10A-Er-Src	breast:	n/a
38	chr15:45479755-45479805	SKMC	muscle:	n/a
39	chr15:45479755-45479805	GM12891	blood:	n/a
40	chr15:45479755-45479805	PANC-1	pancreas:	n/a
41	chr15:45479755-45479805	PFSK-1	brain:	n/a
42	chr15:45479755-45479805	AG09309	skin:	n/a
43	chr15:45479755-45479805	AG10803	skin:	n/a
44	chr15:45479755-45479805	GM12892	blood:	n/a
45	chr15:45479755-45479805	HCF	heart:	n/a
46	chr15:45479755-45479805	HCT-116	colon:	n/a
47	chr15:45479755-45479805	HNPCEpiC	eye:	n/a
48	chr15:45479755-45479805	GM12878	blood:	n/a
49	chr15:45479755-45479805	A549	lung:	n/a
50	chr15:45479755-45479805	HRCEpiC	kidney:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45465361..45468029-chr15:45478692..45480743,2	MCF-7	breast:
2	chr15:45457736..45460170-chr15:45478587..45480947,2	MCF-7	breast:
3	chr15:45457275..45460718-chr15:45477484..45481344,4	K562	blood:
4	chr15:45457610..45461525-chr15:45477333..45480560,5	MCF-7	breast:
5	chr15:45478077..45482452-chr15:45491020..45494377,5	MCF-7	breast:
6	chr15:45458222..45460718-chr15:45477355..45481212,4	K562	blood:
7	chr15:45465443..45468186-chr15:45479581..45482219,2	MCF-7	breast:
8	chr15:45461602..45463661-chr15:45476012..45479858,4	K562	blood:
9	chr15:45477456..45480320-chr15:45491100..45493481,2	MCF-7	breast:
10	chr15:45471595..45473672-chr15:45478332..45480462,2	MCF-7	breast:

No data

Variant related genes	Relation type
SHF	TF binding region
SHF	CpG island
ENSG00000259539	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000138606	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	esv3339591	chr15:45478685-45481233	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
9	esv3450392	chr15:45479060-45481133	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45473200-45480400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:45476000-45480200	Weak transcription	K562	blood
3	chr15:45477200-45480400	Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr15:45477400-45479800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:45477800-45479800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:45478000-45480200	Enhancers	Placenta	Placenta
7	chr15:45478200-45479800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr15:45478200-45480600	Active TSS	Fetal Kidney	kidney
9	chr15:45478600-45479800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:45478600-45479800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr15:45478800-45479800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:45478800-45479800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr15:45478800-45480400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:45478800-45480400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:45479000-45479800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:45479000-45479800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:45479000-45479800	Flanking Active TSS	Dnd41	blood
18	chr15:45479000-45480400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr15:45479000-45480600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr15:45479000-45481000	Active TSS	Ovary	ovary
21	chr15:45479000-45481200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr15:45479200-45479800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr15:45479200-45480000	Weak transcription	HMEC	breast
24	chr15:45479200-45480200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr15:45479200-45480200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:45479200-45480200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr15:45479200-45480400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:45479200-45480400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr15:45479200-45480400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr15:45479200-45480400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:45479200-45480400	Active TSS	Psoas Muscle	Psoas
32	chr15:45479200-45480400	Bivalent/Poised TSS	GM12878-XiMat	blood
33	chr15:45479200-45480400	Active TSS	HUVEC	blood vessel
34	chr15:45479200-45480600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:45479200-45480600	Active TSS	Aorta	Aorta
36	chr15:45479200-45480600	Active TSS	Brain Substantia Nigra	brain
37	chr15:45479200-45480600	Active TSS	Fetal Lung	lung
38	chr15:45479200-45480600	Active TSS	Gastric	stomach
39	chr15:45479200-45480600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr15:45479200-45480800	Active TSS	Brain Germinal Matrix	brain
41	chr15:45479200-45480800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:45479200-45481000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:45479200-45481000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr15:45479400-45479800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr15:45479400-45479800	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr15:45479400-45479800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:45479400-45479800	Bivalent/Poised TSS	Fetal Brain Female	brain
48	chr15:45479400-45479800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr15:45479400-45479800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr15:45479400-45480000	Active TSS	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links