Variant report

Variant	rs45461294
Chromosome Location	chr15:39884667-39884668
allele	A/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	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:39884523-39886945	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
4	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr15:39884616-39886183	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
7	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr15:39884516-39886887	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
12	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
13	RAD21	chr15:39884605-39884692	A549	lung:	n/a	n/a
14	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
15	POLR2A	chr15:39884508-39887110	MCF-7	breast:	n/a	n/a
16	POLR2A	chr15:39883090-39885893	HepG2	liver:	n/a	n/a
17	POLR2A	chr15:39884481-39886919	HUVEC	blood vessel:	n/a	n/a
18	JUN	chr15:39884527-39884724	K562	blood:	n/a	n/a
19	POLR2A	chr15:39877424-39887319	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr15:39884658-39887138	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:39884664-39885137	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
THBS1	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1038097	0.94[EUR][1000 genomes]
rs1051442	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10520141	0.95[EUR][1000 genomes]
rs10520143	0.90[EUR][1000 genomes]
rs10520146	0.83[EUR][1000 genomes]
rs1382443	0.94[EUR][1000 genomes]
rs1382444	0.94[EUR][1000 genomes]
rs16969487	0.95[EUR][1000 genomes]
rs16969491	0.94[EUR][1000 genomes]
rs16969547	0.84[EUR][1000 genomes]
rs17632916	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633107	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17633210	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17705806	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17706083	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17706179	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1813493	0.94[EUR][1000 genomes]
rs1988082	0.85[EUR][1000 genomes]
rs1988555	0.88[EUR][1000 genomes]
rs2228263	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2411316	0.95[EUR][1000 genomes]
rs2618156	0.94[EUR][1000 genomes]
rs2618160	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618161	0.94[EUR][1000 genomes]
rs2618164	0.96[EUR][1000 genomes]
rs2618165	0.96[EUR][1000 genomes]
rs2618167	0.94[EUR][1000 genomes]
rs2664123	0.95[EUR][1000 genomes]
rs2664136	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664137	0.94[EUR][1000 genomes]
rs2664138	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664140	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664142	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377784	0.95[EUR][1000 genomes]
rs28549326	0.95[EUR][1000 genomes]
rs28619289	0.95[EUR][1000 genomes]
rs28653011	0.95[EUR][1000 genomes]
rs34878675	0.90[EUR][1000 genomes]
rs41315060	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4415979	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4503768	0.88[EUR][1000 genomes]
rs4923835	0.88[EUR][1000 genomes]
rs58188999	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59578395	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59628570	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6492905	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74008647	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74008648	0.95[EUR][1000 genomes]
rs880270	0.95[EUR][1000 genomes]
rs954152	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972350	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39873400-39886800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
3	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
4	chr15:39875200-39887800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:39875400-39886000	Weak transcription	Psoas Muscle	Psoas
8	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:39876000-39886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:39876000-39886600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:39876000-39886800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:39876000-39888600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:39876200-39888200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:39876400-39886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:39876600-39886400	Strong transcription	Lung	lung
21	chr15:39876800-39885200	Weak transcription	Small Intestine	intestine
22	chr15:39877000-39887600	Weak transcription	Brain Germinal Matrix	brain
23	chr15:39877200-39886000	Strong transcription	A549	lung
24	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:39877800-39887200	Weak transcription	Fetal Thymus	thymus
26	chr15:39877800-39888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:39877800-39888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:39878000-39888400	Strong transcription	Left Ventricle	heart
29	chr15:39878000-39890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:39878200-39886800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr15:39878200-39888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:39878400-39888400	Strong transcription	NHEK	skin
33	chr15:39878600-39888400	Strong transcription	HepG2	liver
34	chr15:39878600-39888800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr15:39879000-39888800	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:39879200-39888400	Strong transcription	Adipose Nuclei	Adipose
37	chr15:39879200-39888400	Strong transcription	Fetal Lung	lung
38	chr15:39879600-39884800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:39879800-39886200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:39879800-39889400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:39880000-39886200	Strong transcription	Placenta	Placenta
42	chr15:39880000-39888000	Strong transcription	Fetal Heart	heart
43	chr15:39880200-39884800	Strong transcription	NH-A	brain
44	chr15:39880200-39889400	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr15:39880400-39885600	Weak transcription	Stomach Mucosa	stomach
46	chr15:39880600-39887800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:39880600-39887800	Strong transcription	Ovary	ovary
48	chr15:39880800-39886600	Strong transcription	Fetal Stomach	stomach
49	chr15:39880800-39888600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:39880800-39890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links