Variant report

Variant	rs28658414
Chromosome Location	chr15:72498228-72498229
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:72498222-72498304	A549	lung:	n/a	n/a
2	POLR2A	chr15:72498217-72501459	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr15:72498027-72500773	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:72498099-72500623	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:72490228-72501294	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:72498005-72500706	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:72498163-72501330	K562	blood:	n/a	n/a
8	POLR2A	chr15:72498096-72498412	HCT-116	colon:	n/a	n/a
9	POLR2A	chr15:72498152-72500954	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:72498152-72499455	HL-60	blood:	n/a	n/a
11	POLR2A	chr15:72488837-72501457	U87	brain:	n/a	n/a
12	POLR2A	chr15:72498219-72498577	HepG2	liver:	n/a	n/a
13	POLR2A	chr15:72488735-72501628	U87	brain:	n/a	n/a
14	POLR2A	chr15:72490001-72501490	GM12891	blood:	n/a	n/a
15	POLR2A	chr15:72498174-72498661	A549	lung:	n/a	n/a
16	POLR2A	chr15:72488802-72501457	U87	brain:	n/a	n/a
17	POLR2A	chr15:72498010-72498350	HCT-116	colon:	n/a	n/a
18	POLR2A	chr15:72489740-72498760	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr15:72498023-72501355	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:72488729-72501598	U87	brain:	n/a	n/a
21	POLR2A	chr15:72497975-72501492	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr15:72498150-72498772	K562	blood:	n/a	n/a
23	POLR2A	chr15:72489656-72501421	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:72498082-72501381	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:72498195-72501286	A549	lung:	n/a	n/a
26	POLR2A	chr15:72497781-72501382	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr15:72498096-72501429	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:72498105-72500724	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72498006..72500536-chr15:72520929..72523260,2	K562	blood:
2	chr15:72497804..72499839-chr15:72765083..72768033,2	K562	blood:
3	chr15:72489508..72492052-chr15:72496693..72498858,2	MCF-7	breast:
4	chr15:72493161..72495075-chr15:72496784..72499143,2	K562	blood:
5	chr15:72494801..72498747-chr15:72521044..72524691,4	K562	blood:
6	chr15:72497368..72499255-chr15:72501024..72504007,2	K562	blood:
7	chr15:72497368..72499511-chr15:72501024..72504196,4	K562	blood:
8	chr15:72497728..72499574-chr6:26124420..26126089,2	MCF-7	breast:
9	chr15:72495998..72498558-chr15:72562827..72566042,3	MCF-7	breast:

No data

Variant related genes	Relation type
PKM	TF binding region
ENSG00000175318	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs13329116	1.00[AMR][1000 genomes]
rs13329270	1.00[AMR][1000 genomes]
rs13329340	1.00[AMR][1000 genomes]
rs28367264	1.00[AMR][1000 genomes]
rs28373432	1.00[AMR][1000 genomes]
rs28378260	1.00[AMR][1000 genomes]
rs28393460	1.00[AMR][1000 genomes]
rs28396234	1.00[AMR][1000 genomes]
rs28397237	1.00[AMR][1000 genomes]
rs28403882	1.00[AMR][1000 genomes]
rs28408067	1.00[AMR][1000 genomes]
rs28429589	1.00[AMR][1000 genomes]
rs28448787	1.00[AMR][1000 genomes]
rs28450008	1.00[AMR][1000 genomes]
rs28450424	1.00[AMR][1000 genomes]
rs28451732	1.00[AMR][1000 genomes]
rs28455090	1.00[AMR][1000 genomes]
rs28456991	1.00[AMR][1000 genomes]
rs28482979	1.00[AMR][1000 genomes]
rs28483934	1.00[AMR][1000 genomes]
rs28504509	1.00[AMR][1000 genomes]
rs28542557	1.00[AMR][1000 genomes]
rs28543029	1.00[AMR][1000 genomes]
rs28547979	1.00[AMR][1000 genomes]
rs28548453	1.00[AMR][1000 genomes]
rs28552371	1.00[AMR][1000 genomes]
rs28553452	1.00[AMR][1000 genomes]
rs28569017	1.00[AMR][1000 genomes]
rs28573725	1.00[AMR][1000 genomes]
rs28583168	1.00[AMR][1000 genomes]
rs28589979	1.00[AMR][1000 genomes]
rs28605814	1.00[AMR][1000 genomes]
rs28628140	1.00[AMR][1000 genomes]
rs28628792	1.00[AMR][1000 genomes]
rs28634283	1.00[AMR][1000 genomes]
rs28636054	1.00[AMR][1000 genomes]
rs28639590	1.00[AMR][1000 genomes]
rs28642081	1.00[AMR][1000 genomes]
rs28643436	1.00[AMR][1000 genomes]
rs28654851	1.00[AMR][1000 genomes]
rs28654861	1.00[AMR][1000 genomes]
rs28657431	1.00[AMR][1000 genomes]
rs28660217	1.00[AMR][1000 genomes]
rs28660581	1.00[AMR][1000 genomes]
rs28663692	1.00[AMR][1000 genomes]
rs28667521	1.00[AMR][1000 genomes]
rs28675378	1.00[AMR][1000 genomes]
rs28701136	1.00[AMR][1000 genomes]
rs28707151	1.00[AMR][1000 genomes]
rs28707565	1.00[AMR][1000 genomes]
rs28725348	1.00[AMR][1000 genomes]
rs28727443	1.00[AMR][1000 genomes]
rs28741048	1.00[AMR][1000 genomes]
rs28791192	1.00[AMR][1000 genomes]
rs28801155	1.00[AMR][1000 genomes]
rs28808678	1.00[AMR][1000 genomes]
rs28824293	1.00[AMR][1000 genomes]
rs28833566	1.00[AMR][1000 genomes]
rs28853032	1.00[AMR][1000 genomes]
rs28872877	1.00[AMR][1000 genomes]
rs28879707	1.00[AMR][1000 genomes]
rs8192372	1.00[AMR][1000 genomes]
rs9920204	1.00[AMR][1000 genomes]
rs9920223	1.00[AMR][1000 genomes]
rs9920987	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
4	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 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	chr15:72490000-72501800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:72490000-72507600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:72490400-72504000	Genic enhancers	A549	lung
4	chr15:72490400-72512000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:72490600-72498400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:72490600-72499400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:72490600-72503400	Strong transcription	Primary B cells from cord blood	blood
8	chr15:72490600-72508200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:72490600-72512000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:72490600-72513000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:72490600-72513200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:72490600-72513600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:72490600-72513800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:72490600-72515600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:72490600-72518000	Strong transcription	Dnd41	blood
16	chr15:72490800-72504400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:72490800-72504400	Strong transcription	Colonic Mucosa	Colon
18	chr15:72490800-72511800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:72490800-72511800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:72490800-72511800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:72490800-72512200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:72490800-72513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:72490800-72513000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:72490800-72514200	Strong transcription	Primary T cells from cord blood	blood
25	chr15:72490800-72514400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:72490800-72518400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:72491000-72502800	Strong transcription	Pancreas	Pancrea
28	chr15:72491000-72504800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:72491000-72504800	Strong transcription	Aorta	Aorta
30	chr15:72491000-72511600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:72491000-72512200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:72491000-72512200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:72491000-72512600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr15:72491000-72512600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:72491000-72513000	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr15:72491000-72513400	Strong transcription	Fetal Lung	lung
37	chr15:72491000-72513600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:72491000-72513600	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr15:72491000-72513800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:72491000-72513800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:72491000-72514600	Strong transcription	K562	blood
42	chr15:72491200-72512000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:72491200-72512000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:72491200-72512800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:72491200-72513000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:72491400-72501000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:72491400-72511600	Strong transcription	Ovary	ovary
48	chr15:72491400-72512400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:72491600-72501400	Genic enhancers	HMEC	breast
50	chr15:72491600-72511200	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links