Variant report

Variant	rs542540098
Chromosome Location	chr15:52311374-52311375
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	POLR2A	chr15:52311094-52312216	GM10847	blood:	n/a	n/a
2	JUND	chr15:52311328-52311528	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr15:52311178-52311538	HepG2	liver:	n/a	n/a
4	CTCF	chr15:52311300-52311450	GM12873	blood:	n/a	n/a
5	EGR1	chr15:52311043-52311605	K562	blood:	n/a	chr15:52311342-52311355 chr15:52311342-52311355 chr15:52311406-52311419 chr15:52311345-52311354 chr15:52311343-52311357 chr15:52311406-52311419 chr15:52311342-52311355 chr15:52311342-52311356 chr15:52311340-52311350 chr15:52311342-52311355 chr15:52311380-52311393 chr15:52311341-52311356 chr15:52311405-52311420 chr15:52311404-52311414 chr15:52311380-52311393 chr15:52311338-52311360 chr15:52311345-52311355 chr15:52311379-52311394 chr15:52311270-52311284
6	SMARCC1	chr15:52310695-52311541	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:52310865-52311810	U87	brain:	n/a	n/a
8	POLR2A	chr15:52310923-52311766	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:52310967-52312494	HUVEC	blood vessel:	n/a	n/a
10	TEAD4	chr15:52310932-52311649	A549	lung:	n/a	n/a
11	YY1	chr15:52311176-52311870	GM12878	blood:	n/a	chr15:52311282-52311296 chr15:52311344-52311353 chr15:52311281-52311295 chr15:52311484-52311495 chr15:52311405-52311414
12	BCL3	chr15:52311089-52311640	GM12878	blood:	n/a	chr15:52311281-52311294 chr15:52311277-52311286 chr15:52311340-52311353 chr15:52311283-52311296
13	FOSL2	chr15:52311041-52311534	A549	lung:	n/a	n/a
14	POLR2A	chr15:52310872-52311769	Hela-S3	cervix:	n/a	n/a
15	YY1	chr15:52310997-52311707	H1-hESC	embryonic stem cell:	n/a	chr15:52311282-52311296 chr15:52311344-52311353 chr15:52311281-52311295 chr15:52311484-52311495 chr15:52311405-52311414
16	YY1	chr15:52311212-52311789	ECC-1	luminal epithelium:	n/a	chr15:52311282-52311296 chr15:52311344-52311353 chr15:52311281-52311295 chr15:52311484-52311495 chr15:52311405-52311414
17	REST	chr15:52311049-52311775	PFSK-1	brain:	n/a	n/a
18	CREB1	chr15:52311034-52311788	GM12878	blood:	n/a	n/a
19	TBP	chr15:52311076-52312864	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:52310700-52313695	GM12878	blood:	n/a	n/a
21	GTF3C2	chr15:52311157-52312306	K562	blood:	n/a	n/a
22	E2F1	chr15:52311053-52312253	Hela-S3	cervix:	n/a	chr15:52311347-52311359 chr15:52311405-52311414 chr15:52311704-52311714 chr15:52311918-52311928 chr15:52311906-52311915 chr15:52311459-52311467 chr15:52312011-52312021 chr15:52311347-52311358
23	STAT5A	chr15:52310947-52311633	GM12878	blood:	n/a	chr15:52311338-52311350 chr15:52311414-52311426 chr15:52311209-52311217
24	EP300	chr15:52311153-52311619	T-47D	breast:	n/a	chr15:52311327-52311343
25	POLR2A	chr15:52311051-52312114	HCT-116	colon:	n/a	n/a
26	POLR2A	chr15:52310849-52312297	Raji	blood:	n/a	n/a
27	SIN3AK20	chr15:52311061-52312341	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr15:52310853-52312523	K562	blood:	n/a	n/a
29	POLR2A	chr15:52311072-52311757	ECC-1	luminal epithelium:	n/a	n/a
30	TAF1	chr15:52311303-52311612	GM12891	blood:	n/a	n/a
31	NFYA	chr15:52310898-52311453	Hela-S3	cervix:	n/a	n/a
32	REST	chr15:52310736-52312948	H1-neurons	neurons:	n/a	chr15:52311953-52311966
33	SIN3AK20	chr15:52311007-52311620	K562	blood:	n/a	n/a
34	TAF1	chr15:52310910-52311797	MCF-7	breast:	n/a	n/a
35	REST	chr15:52311006-52311796	HL-60	blood:	n/a	n/a
36	SRF	chr15:52311069-52311624	ECC-1	luminal epithelium:	n/a	chr15:52311406-52311416
37	PML	chr15:52310843-52311662	K562	blood:	n/a	n/a
38	TAF1	chr15:52311103-52311682	GM12878	blood:	n/a	n/a
39	BACH1	chr15:52310982-52311474	K562	blood:	n/a	n/a
40	RELA	chr15:52311142-52311655	GM12892	blood:	n/a	chr15:52311311-52311320 chr15:52311311-52311320
41	NFIC	chr15:52310905-52311598	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:52310863-52311717	K562	blood:	n/a	n/a
43	SIN3A	chr15:52311072-52311620	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:52311046-52311797	SK-N-SH	brain:	n/a	n/a
45	TAF1	chr15:52311126-52311826	GM12878	blood:	n/a	n/a
46	BCLAF1	chr15:52310997-52311760	GM12878	blood:	n/a	chr15:52311281-52311294 chr15:52311277-52311286 chr15:52311340-52311353 chr15:52311702-52311715 chr15:52311283-52311296
47	POLR2A	chr15:52310883-52311797	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr15:52310834-52312878	GM12878	blood:	n/a	n/a
49	TEAD4	chr15:52310983-52311626	ECC-1	luminal epithelium:	n/a	n/a
50	EBF1	chr15:52311015-52311478	GM12878	blood:	n/a	chr15:52311236-52311247

No.	Distal block	Cell Line	Cell type
1	chr15:52311192..52314853-chr15:52323962..52330649,8	K562	blood:
2	chr15:52310998..52312915-chr15:52428801..52431088,2	MCF-7	breast:
3	chr15:52310752..52311563-chr15:80215677..80216555,2	Hela-S3	cervix:
4	chr15:52175882..52177402-chr15:52311052..52312787,2	K562	blood:
5	chr15:52309643..52312109-chr15:52424380..52429568,4	MCF-7	breast:
6	chr15:52310228..52314421-chr15:52470196..52474583,10	MCF-7	breast:
7	chr15:51914606..51918105-chr15:52309438..52311518,3	K562	blood:
8	chr15:52309956..52312123-chr15:52404856..52406463,2	MCF-7	breast:
9	chr15:52029435..52031649-chr15:52311154..52313570,2	K562	blood:
10	chr15:52310337..52312699-chr15:76160460..76162429,2	MCF-7	breast:
11	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:
12	chr15:52310908..52311894-chr6:26158225..26159035,2	Hela-S3	cervix:
13	chr1:186344295..186345189-chr15:52311029..52311907,2	Hela-S3	cervix:
14	chr15:50646379..50648105-chr15:52310964..52313763,2	MCF-7	breast:
15	chr15:52308069..52314807-chr15:52359242..52376066,34	MCF-7	breast:
16	chr15:52262145..52266701-chr15:52309209..52314377,19	MCF-7	breast:
17	chr1:149857624..149859887-chr15:52308865..52312483,3	MCF-7	breast:
18	chr15:51913842..51915651-chr15:52310480..52312908,3	MCF-7	breast:
19	chr15:52311066..52311781-chr16:28564992..28565495,2	MCF-7	breast:
20	chr15:52262263..52265564-chr15:52309489..52315686,9	K562	blood:
21	chr15:52309759..52313480-chr15:52429073..52432426,3	K562	blood:
22	chr15:52311231..52311963-chr2:198317889..198318505,2	Hela-S3	cervix:
23	chr11:9481906..9482892-chr15:52311101..52311641,2	Hela-S3	cervix:
24	chr1:150551175..150551879-chr15:52310855..52311822,2	Hela-S3	cervix:
25	chr15:52262270..52265607-chr15:52309730..52314612,10	K562	blood:
26	chr15:52311211..52313546-chr15:52470591..52472771,2	MCF-7	breast:
27	chr13:113861573..113863819-chr15:52310834..52313167,2	MCF-7	breast:
28	chr15:52311260..52311978-chr17:4851077..4851818,2	Hela-S3	cervix:
29	chr12:76953528..76954278-chr15:52311179..52311706,2	Hela-S3	cervix:
30	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259438	TF binding region
MAPK6	TF binding region
ENSG00000104093	Chromatin interaction
ENSG00000140280	Chromatin interaction
ENSG00000259178	Chromatin interaction
ENSG00000180953	Chromatin interaction
ENSG00000047410	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000259332	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000126226	Chromatin interaction
ENSG00000137875	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000157181	Chromatin interaction
ENSG00000176476	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000139842	Chromatin interaction
ENSG00000108515	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000207484	Chromatin interaction
ENSG00000115520	Chromatin interaction
ENSG00000259398	Chromatin interaction
ENSG00000259712	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000140367	Chromatin interaction
ENSG00000091039	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000242327	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000166477	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	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv3330502	chr15:52310485-52313033	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 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	chr15:52310400-52311400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:52310600-52311400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:52310600-52311400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr15:52310600-52313200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:52310600-52313800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:52310600-52313800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr15:52310600-52313800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr15:52310800-52311400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:52310800-52311400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:52310800-52311400	Flanking Active TSS	Colonic Mucosa	Colon
11	chr15:52310800-52311400	Flanking Active TSS	Dnd41	blood
12	chr15:52310800-52311400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr15:52310800-52311400	Flanking Active TSS	NH-A	brain
14	chr15:52310800-52312800	Active TSS	Fetal Kidney	kidney
15	chr15:52310800-52312800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr15:52310800-52313000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:52310800-52313000	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr15:52310800-52313000	Active TSS	Liver	Liver
19	chr15:52310800-52313000	Active TSS	Brain Angular Gyrus	brain
20	chr15:52310800-52313000	Active TSS	Brain Hippocampus Middle	brain
21	chr15:52310800-52313400	Active TSS	Aorta	Aorta
22	chr15:52310800-52313600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:52310800-52313800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr15:52310800-52313800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:52310800-52314200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:52310800-52314800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:52310800-52314800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr15:52311000-52312000	Active TSS	Primary hematopoietic stem cells	blood
29	chr15:52311000-52312200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr15:52311000-52312600	Active TSS	Gastric	stomach
31	chr15:52311000-52312800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:52311000-52312800	Active TSS	Ovary	ovary
33	chr15:52311000-52312800	Active TSS	Small Intestine	intestine
34	chr15:52311000-52313000	Active TSS	Placenta Amnion	Placenta Amnion
35	chr15:52311000-52313600	Active TSS	H9 Cell Line	embryonic stem cell
36	chr15:52311000-52313600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:52311200-52311400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:52311200-52311400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:52311200-52311400	Enhancers	Fetal Brain Male	brain
40	chr15:52311200-52311400	Active TSS	Stomach Mucosa	stomach
41	chr15:52311200-52311600	Transcr. at gene 5' and 3'	Right Atrium	heart
42	chr15:52311200-52312000	Active TSS	Primary B cells from cord blood	blood
43	chr15:52311200-52312000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:52311200-52312000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:52311200-52312000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:52311200-52312000	Active TSS	Brain Germinal Matrix	brain
47	chr15:52311200-52312200	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr15:52311200-52312200	Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr15:52311200-52312200	Active TSS	Primary B cells from peripheral blood	blood
50	chr15:52311200-52312200	Active TSS	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links