Variant report

Variant	rs564360219
Chromosome Location	chr15:52311021-52311022
allele	G/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	SMARCC1	chr15:52310695-52311541	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:52310865-52311810	U87	brain:	n/a	n/a
3	POLR2A	chr15:52310923-52311766	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:52310967-52312494	HUVEC	blood vessel:	n/a	n/a
5	TEAD4	chr15:52310932-52311649	A549	lung:	n/a	n/a
6	CEBPB	chr15:52311012-52311341	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr15:52310872-52311769	Hela-S3	cervix:	n/a	n/a
8	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
9	POLR2A	chr15:52310700-52313695	GM12878	blood:	n/a	n/a
10	STAT5A	chr15:52310947-52311633	GM12878	blood:	n/a	chr15:52311338-52311350 chr15:52311414-52311426 chr15:52311209-52311217
11	WRNIP1	chr15:52310958-52311310	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:52310849-52312297	Raji	blood:	n/a	n/a
13	POLR2A	chr15:52310853-52312523	K562	blood:	n/a	n/a
14	NFYA	chr15:52310898-52311453	Hela-S3	cervix:	n/a	n/a
15	REST	chr15:52310736-52312948	H1-neurons	neurons:	n/a	chr15:52311953-52311966
16	SIN3AK20	chr15:52311007-52311620	K562	blood:	n/a	n/a
17	TAF1	chr15:52310910-52311797	MCF-7	breast:	n/a	n/a
18	REST	chr15:52311006-52311796	HL-60	blood:	n/a	n/a
19	PML	chr15:52310843-52311662	K562	blood:	n/a	n/a
20	BACH1	chr15:52310982-52311474	K562	blood:	n/a	n/a
21	NFIC	chr15:52310905-52311598	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:52310863-52311717	K562	blood:	n/a	n/a
23	BCLAF1	chr15:52310997-52311760	GM12878	blood:	n/a	chr15:52311281-52311294 chr15:52311277-52311286 chr15:52311340-52311353 chr15:52311702-52311715 chr15:52311283-52311296
24	POLR2A	chr15:52310883-52311797	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr15:52310834-52312878	GM12878	blood:	n/a	n/a
26	TEAD4	chr15:52310983-52311626	ECC-1	luminal epithelium:	n/a	n/a
27	EBF1	chr15:52311015-52311478	GM12878	blood:	n/a	chr15:52311236-52311247
28	TBP	chr15:52310893-52311670	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF2	chr15:52310949-52311423	Hela-S3	cervix:	n/a	n/a
30	SP1	chr15:52310883-52311772	A549	lung:	n/a	chr15:52311385-52311395 chr15:52311385-52311395 chr15:52311404-52311414 chr15:52311404-52311413 chr15:52311404-52311414 chr15:52311340-52311352 chr15:52311403-52311415 chr15:52311410-52311424 chr15:52311405-52311414 chr15:52311404-52311418 chr15:52311346-52311357 chr15:52311404-52311413 chr15:52311403-52311415 chr15:52311347-52311356
31	ATF2	chr15:52310959-52311514	GM12878	blood:	n/a	n/a
32	MTA3	chr15:52310826-52311614	GM12878	blood:	n/a	n/a
33	RFX5	chr15:52310994-52311487	GM12878	blood:	n/a	n/a
34	GATA3	chr15:52310883-52312485	MCF-7	breast:	n/a	chr15:52312122-52312129
35	MAX	chr15:52310847-52311663	K562	blood:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
36	TEAD4	chr15:52311003-52311516	HepG2	liver:	n/a	n/a
37	POLR2A	chr15:52310709-52311693	GM12878	blood:	n/a	n/a
38	MAX	chr15:52310918-52311612	NB4	blood:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
39	MXI1	chr15:52310700-52314090	SK-N-SH	brain:	n/a	n/a
40	CREB1	chr15:52310916-52311657	HepG2	liver:	n/a	n/a
41	POLR2A	chr15:52310959-52311723	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr15:52310908-52311783	HUVEC	blood vessel:	n/a	n/a
43	CTCF	chr15:52310980-52311130	A549	lung:	n/a	n/a
44	ZKSCAN1	chr15:52310606-52311627	Hela-S3	cervix:	n/a	n/a
45	CHD1	chr15:52310864-52311657	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:52310992-52312477	K562	blood:	n/a	n/a
47	E2F6	chr15:52311019-52311620	A549	lung:	n/a	chr15:52311347-52311359 chr15:52311405-52311414 chr15:52311459-52311467
48	TEAD4	chr15:52310952-52311639	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr15:52310902-52312332	HL-60	blood:	n/a	n/a
50	EGR1	chr15:52310994-52311624	ECC-1	luminal epithelium:	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

No.	Distal block	Cell Line	Cell type
1	chr15:52310998..52312915-chr15:52428801..52431088,2	MCF-7	breast:
2	chr15:52310752..52311563-chr15:80215677..80216555,2	Hela-S3	cervix:
3	chr15:52309643..52312109-chr15:52424380..52429568,4	MCF-7	breast:
4	chr15:52310228..52314421-chr15:52470196..52474583,10	MCF-7	breast:
5	chr15:51914606..51918105-chr15:52309438..52311518,3	K562	blood:
6	chr15:52309956..52312123-chr15:52404856..52406463,2	MCF-7	breast:
7	chr15:52310337..52312699-chr15:76160460..76162429,2	MCF-7	breast:
8	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:
9	chr15:52310908..52311894-chr6:26158225..26159035,2	Hela-S3	cervix:
10	chr15:50646379..50648105-chr15:52310964..52313763,2	MCF-7	breast:
11	chr15:52308069..52314807-chr15:52359242..52376066,34	MCF-7	breast:
12	chr15:52262145..52266701-chr15:52309209..52314377,19	MCF-7	breast:
13	chr1:149857624..149859887-chr15:52308865..52312483,3	MCF-7	breast:
14	chr15:51913842..51915651-chr15:52310480..52312908,3	MCF-7	breast:
15	chr15:52262263..52265564-chr15:52309489..52315686,9	K562	blood:
16	chr15:52309759..52313480-chr15:52429073..52432426,3	K562	blood:
17	chr1:150551175..150551879-chr15:52310855..52311822,2	Hela-S3	cervix:
18	chr15:52262270..52265607-chr15:52309730..52314612,10	K562	blood:
19	chr13:113861573..113863819-chr15:52310834..52313167,2	MCF-7	breast:
20	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LEO1-3	chr15:52310896-52311292	ENSG00000259438.1

Variant related genes	Relation type
MAPK6	TF binding region
ENSG00000158373	Chromatin interaction
ENSG00000259712	Chromatin interaction
ENSG00000242327	Chromatin interaction
ENSG00000137875	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000259332	Chromatin interaction
ENSG00000180953	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000140367	Chromatin interaction
ENSG00000126226	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000139842	Chromatin interaction
ENSG00000259178	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000178096	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	chr15:52310600-52311200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:52310600-52311200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:52310600-52311200	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr15:52310600-52311200	Flanking Active TSS	Fetal Brain Male	brain
6	chr15:52310600-52311200	Flanking Active TSS	GM12878-XiMat	blood
7	chr15:52310600-52311200	Flanking Active TSS	Hela-S3	cervix
8	chr15:52310600-52311200	Flanking Active TSS	HepG2	liver
9	chr15:52310600-52311200	Flanking Active TSS	K562	blood
10	chr15:52310600-52311400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:52310600-52311400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr15:52310600-52313200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr15:52310600-52313800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:52310600-52313800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr15:52310600-52313800	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr15:52310800-52311200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:52310800-52311200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:52310800-52311200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:52310800-52311200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr15:52310800-52311200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:52310800-52311200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:52310800-52311200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr15:52310800-52311200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr15:52310800-52311200	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr15:52310800-52311200	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr15:52310800-52311200	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr15:52310800-52311200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr15:52310800-52311200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:52310800-52311200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr15:52310800-52311200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr15:52310800-52311200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:52310800-52311200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr15:52310800-52311200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr15:52310800-52311200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:52310800-52311200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:52310800-52311200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr15:52310800-52311200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:52310800-52311200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:52310800-52311200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:52310800-52311200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr15:52310800-52311200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr15:52310800-52311200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:52310800-52311200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:52310800-52311200	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr15:52310800-52311200	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr15:52310800-52311200	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr15:52310800-52311200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr15:52310800-52311200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:52310800-52311200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr15:52310800-52311200	Flanking Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links