Variant report

Variant	rs542523169
Chromosome Location	chr15:59729708-59729709
allele	C/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	MYC	chr15:59729645-59731187	A549	lung:	n/a	chr15:59730613-59730623
2	MAX	chr15:59729592-59730944	ECC-1	luminal epithelium:	n/a	chr15:59730613-59730623
3	MAX	chr15:59729585-59730996	ECC-1	luminal epithelium:	n/a	chr15:59730613-59730623
4	MTA3	chr15:59729471-59730302	GM12878	blood:	n/a	n/a
5	MXI1	chr15:59729481-59731090	SK-N-SH	brain:	n/a	chr15:59730227-59730242 chr15:59730225-59730240
6	E2F6	chr15:59729701-59731015	A549	lung:	n/a	chr15:59730703-59730713 chr15:59730699-59730707 chr15:59730077-59730086 chr15:59730699-59730707 chr15:59730694-59730709 chr15:59730698-59730708 chr15:59730432-59730441
7	REST	chr15:59729594-59730960	H1-neurons	neurons:	n/a	n/a
8	SIN3A	chr15:59729615-59730930	H1-hESC	embryonic stem cell:	n/a	chr15:59730406-59730419 chr15:59730407-59730416 chr15:59730522-59730533
9	SMARCB1	chr15:59729699-59730903	Hela-S3	cervix:	n/a	n/a
10	MAX	chr15:59729565-59731594	A549	lung:	n/a	chr15:59730613-59730623
11	CTCF	chr15:59729620-59729770	GM12874	blood:	n/a	n/a
12	HA-E2F1	chr15:59729622-59730862	Hela-S3	cervix:	n/a	chr15:59730703-59730713 chr15:59730699-59730707 chr15:59730077-59730086 chr15:59730699-59730707 chr15:59730698-59730708 chr15:59730432-59730441
13	ZEB1	chr15:59729371-59729933	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59662898..59664919-chr15:59728478..59730904,2	MCF-7	breast:

Variant related genes	Relation type
FAM81A	TF binding region
ENSG00000157470	Chromatin interaction
ENSG00000157483	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
4	nsv904278	chr15:59705005-59784648	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv569604	chr15:59729257-59730930	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	esv21135	chr15:59729524-59730974	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59728800-59729800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:59728800-59731800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr15:59729000-59729800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:59729000-59729800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:59729000-59730000	Enhancers	Spleen	Spleen
6	chr15:59729200-59729800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr15:59729200-59729800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:59729200-59729800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
9	chr15:59729200-59730000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr15:59729200-59730000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
11	chr15:59729200-59730000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:59729200-59730000	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr15:59729200-59730000	Flanking Active TSS	Colon Smooth Muscle	Colon
14	chr15:59729200-59730000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
15	chr15:59729200-59730000	Flanking Active TSS	Fetal Brain Male	brain
16	chr15:59729200-59730000	Flanking Active TSS	Right Ventricle	heart
17	chr15:59729200-59730000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr15:59729200-59730000	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr15:59729200-59730200	Flanking Active TSS	GM12878-XiMat	blood
20	chr15:59729200-59730800	Active TSS	Aorta	Aorta
21	chr15:59729200-59730800	Active TSS	Right Atrium	heart
22	chr15:59729200-59731000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:59729200-59731000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr15:59729200-59731400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr15:59729400-59729800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:59729400-59729800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:59729400-59729800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
28	chr15:59729400-59729800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:59729400-59729800	Bivalent Enhancer	Liver	Liver
30	chr15:59729400-59729800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
31	chr15:59729400-59729800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr15:59729400-59729800	Bivalent Enhancer	Placenta	Placenta
33	chr15:59729400-59729800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
34	chr15:59729400-59729800	Bivalent Enhancer	HMEC	breast
35	chr15:59729400-59730000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
36	chr15:59729400-59730000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:59729400-59730000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:59729400-59730000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:59729400-59730000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
40	chr15:59729400-59730000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:59729400-59730000	Flanking Active TSS	Fetal Heart	heart
42	chr15:59729400-59730000	Enhancers	Lung	lung
43	chr15:59729400-59730000	Flanking Active TSS	Ovary	ovary
44	chr15:59729400-59730000	Flanking Active TSS	Psoas Muscle	Psoas
45	chr15:59729400-59730000	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr15:59729400-59730000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr15:59729400-59730000	Enhancers	Small Intestine	intestine
48	chr15:59729400-59730000	Flanking Active TSS	A549	lung
49	chr15:59729400-59730200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:59729400-59730200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links