Variant report

Variant	rs67725996
Chromosome Location	chr15:52471547-52471548
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	POLR2A	chr15:52471409-52472817	GM12891	blood:	n/a	n/a
2	MAX	chr15:52471488-52472365	K562	blood:	n/a	n/a
3	POLR2A	chr15:52471323-52472437	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPD	chr15:52471436-52471819	HepG2	liver:	n/a	n/a
5	TCF12	chr15:52471451-52472429	ECC-1	luminal epithelium:	n/a	chr15:52472246-52472253
6	POLR2A	chr15:52471469-52472414	PFSK-1	brain:	n/a	n/a
7	HDAC2	chr15:52470838-52472694	MCF-7	breast:	n/a	n/a
8	EGR1	chr15:52471499-52472106	K562	blood:	n/a	chr15:52471725-52471735 chr15:52471937-52471947 chr15:52471762-52471776
9	YY1	chr15:52471517-52472543	HepG2	liver:	n/a	chr15:52471844-52471858 chr15:52471725-52471734
10	TCF7L2	chr15:52471476-52472318	HCT-116	colon:	n/a	n/a
11	POLR2A	chr15:52471519-52471802	HUVEC	blood vessel:	n/a	n/a
12	CHD1	chr15:52471187-52471763	GM12878	blood:	n/a	chr15:52471438-52471448
13	POLR2A	chr15:52471251-52472524	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr15:52471499-52472482	ECC-1	luminal epithelium:	n/a	n/a
15	SIN3AK20	chr15:52471537-52471729	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:52471437-52472450	U87	brain:	n/a	n/a
17	RCOR1	chr15:52471421-52472799	IMR90	lung:	n/a	n/a
18	STAT3	chr15:52471506-52471706	MCF10A-Er-Src	breast:	n/a	chr15:52471675-52471686
19	POLR2A	chr15:52471437-52472674	H1-hESC	embryonic stem cell:	n/a	n/a
20	SP1	chr15:52471417-52471841	GM12878	blood:	n/a	chr15:52471440-52471449 chr15:52471622-52471634 chr15:52471439-52471448 chr15:52471623-52471633 chr15:52471623-52471637 chr15:52471439-52471448 chr15:52471441-52471454 chr15:52471624-52471633 chr15:52471622-52471634
21	POLR2A	chr15:52471424-52472526	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:52471487-52472566	MCF-7	breast:	n/a	n/a
23	MAX	chr15:52471498-52472395	H1-hESC	embryonic stem cell:	n/a	n/a
24	USF2	chr15:52471116-52471709	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:52471427-52472425	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr15:52471371-52472427	HCT-116	colon:	n/a	n/a
27	MXI1	chr15:52471445-52471718	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:52471440-52471815	HepG2	liver:	n/a	n/a
29	MYC	chr15:52471488-52472370	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr15:52471524-52472379	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr15:52471503-52472417	A549	lung:	n/a	n/a
32	POLR2A	chr15:52471468-52472754	Raji	blood:	n/a	n/a
33	SMC3	chr15:52471428-52472375	Hela-S3	cervix:	n/a	n/a
34	MXI1	chr15:52471143-52472690	IMR90	lung:	n/a	n/a
35	MAX	chr15:52471419-52472600	HepG2	liver:	n/a	n/a
36	MAZ	chr15:52471369-52472734	GM12878	blood:	n/a	n/a
37	PAX5	chr15:52471520-52471889	GM12892	blood:	n/a	n/a
38	GTF2F1	chr15:52471472-52472291	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr15:52471374-52471849	GM12892	blood:	n/a	n/a
40	ZNF143	chr15:52471439-52471842	GM12878	blood:	n/a	n/a
41	EGR1	chr15:52471547-52472166	K562	blood:	n/a	chr15:52471725-52471735 chr15:52471937-52471947 chr15:52471762-52471776
42	POLR2A	chr15:52471381-52473065	GM12892	blood:	n/a	n/a
43	MAX	chr15:52471260-52472842	A549	lung:	n/a	n/a
44	MAX	chr15:52471534-52472495	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr15:52471519-52471776	HepG2	liver:	n/a	n/a
46	E2F4	chr15:52471279-52472339	MCF10A-Er-Src	breast:	n/a	chr15:52472253-52472267 chr15:52472072-52472087 chr15:52471725-52471734 chr15:52471937-52471946 chr15:52472250-52472264
47	TAF7	chr15:52471528-52472158	H1-hESC	embryonic stem cell:	n/a	n/a
48	STAT5A	chr15:52471066-52471583	GM12878	blood:	n/a	chr15:52471168-52471179
49	POLR2A	chr15:52471501-52472440	HepG2	liver:	n/a	n/a
50	MAX	chr15:52471429-52472429	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52469254..52473137-chr15:52482082..52484822,3	MCF-7	breast:
2	chr15:52471324..52471910-chr17:79849462..79850365,2	Hela-S3	cervix:
3	chr15:52431891..52434316-chr15:52470480..52472199,2	MCF-7	breast:
4	chr15:52262628..52265811-chr15:52469801..52473537,4	MCF-7	breast:
5	chr15:52261233..52265470-chr15:52469433..52474401,7	MCF-7	breast:
6	chr15:52453475..52455065-chr15:52470814..52473297,2	MCF-7	breast:
7	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:
8	chr15:52469891..52472535-chr7:101457623..101459859,2	MCF-7	breast:
9	chr15:52310228..52314421-chr15:52470196..52474583,10	MCF-7	breast:
10	chr15:52311211..52313546-chr15:52470591..52472771,2	MCF-7	breast:
11	chr15:52418174..52420901-chr15:52470720..52473128,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259577	TF binding region
ENSG00000166477	Chromatin interaction
ENSG00000183684	Chromatin interaction
ENSG00000257923	Chromatin interaction
ENSG00000137875	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000141552	Chromatin interaction
ENSG00000206995	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11070882	0.84[EUR][1000 genomes]
rs11856177	0.86[EUR][1000 genomes]
rs12440354	0.81[AMR][1000 genomes]
rs12593936	0.94[EUR][1000 genomes]
rs12593939	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12594809	1.00[ASN][1000 genomes]
rs12595160	0.92[EUR][1000 genomes]
rs12898389	1.00[ASN][1000 genomes]
rs12902522	0.81[AMR][1000 genomes]
rs12904880	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12905698	0.81[AMR][1000 genomes]
rs12909184	0.81[AMR][1000 genomes]
rs12910052	0.81[AMR][1000 genomes]
rs12910398	0.81[AMR][1000 genomes]
rs12916135	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16964750	0.85[AFR][1000 genomes]
rs35712143	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35827106	0.87[EUR][1000 genomes]
rs35914910	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4776007	0.81[AMR][1000 genomes]
rs4776010	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4776011	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776012	0.98[ASN][1000 genomes]
rs4776013	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776014	0.91[EUR][1000 genomes]
rs59289747	0.82[AFR][1000 genomes]
rs66566761	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66757864	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67163040	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67447954	0.81[EUR][1000 genomes]
rs7164508	0.90[EUR][1000 genomes]
rs7172037	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181580	0.95[ASN][1000 genomes]
rs7183278	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73404813	0.81[AFR][1000 genomes]
rs8024311	0.82[AFR][1000 genomes]
rs8025737	0.94[AFR][1000 genomes]
rs8040458	0.80[AFR][1000 genomes]
rs8041504	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52470200-52472800	Active TSS	Brain Anterior Caudate	brain
2	chr15:52470600-52471600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr15:52470600-52471600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr15:52470600-52473000	Active TSS	Brain Angular Gyrus	brain
5	chr15:52470600-52473000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr15:52470600-52473400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:52470800-52471600	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr15:52470800-52471600	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr15:52470800-52471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:52470800-52471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:52470800-52471600	Flanking Active TSS	Dnd41	blood
12	chr15:52470800-52471800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr15:52470800-52472400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:52470800-52472400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:52470800-52472600	Active TSS	Brain Hippocampus Middle	brain
16	chr15:52470800-52473000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:52470800-52473000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr15:52470800-52473200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:52471000-52471600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr15:52471000-52471600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:52471000-52471600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr15:52471000-52471600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr15:52471000-52471600	Flanking Active TSS	Liver	Liver
24	chr15:52471000-52471600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr15:52471000-52471600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
26	chr15:52471000-52471600	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr15:52471000-52471600	Flanking Active TSS	Fetal Thymus	thymus
28	chr15:52471000-52471600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
29	chr15:52471000-52471600	Flanking Active TSS	Thymus	Thymus
30	chr15:52471000-52471600	Flanking Active TSS	HUVEC	blood vessel
31	chr15:52471000-52471600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr15:52471000-52471600	Flanking Active TSS	NH-A	brain
33	chr15:52471000-52471800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr15:52471000-52471800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
35	chr15:52471000-52472000	Active TSS	Colonic Mucosa	Colon
36	chr15:52471000-52472200	Active TSS	NHLF	lung
37	chr15:52471000-52472400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:52471000-52472600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:52471000-52472600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr15:52471000-52472600	Active TSS	Colon Smooth Muscle	Colon
41	chr15:52471000-52472800	Active TSS	Ovary	ovary
42	chr15:52471000-52473000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr15:52471000-52473000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:52471000-52473000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:52471000-52473000	Active TSS	Aorta	Aorta
46	chr15:52471000-52473000	Active TSS	Esophagus	oesophagus
47	chr15:52471200-52471600	Flanking Active TSS	Placenta	Placenta
48	chr15:52471200-52471600	Active TSS	Right Atrium	heart
49	chr15:52471200-52471800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:52471200-52472000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links