Variant report

Variant	rs28501427
Chromosome Location	chr15:52331888-52331889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52317535..52326388-chr15:52327451..52335331,11	K562	blood:
2	chr15:52309828..52312654-chr15:52330668..52332262,2	K562	blood:
3	chr15:52329669..52331948-chr15:52362152..52363907,2	MCF-7	breast:
4	chr15:52331526..52333859-chr15:52340163..52342919,2	K562	blood:
5	chr15:52323591..52325399-chr15:52331469..52333849,2	MCF-7	breast:
6	chr15:52308640..52315286-chr15:52329805..52332909,7	K562	blood:
7	chr15:52331117..52335082-chr15:52360597..52363150,3	K562	blood:
8	chr15:52303163..52304907-chr15:52331339..52333174,2	MCF-7	breast:
9	chr15:52262855..52265387-chr15:52330174..52332552,2	MCF-7	breast:
10	chr15:52308807..52313747-chr15:52329198..52338033,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259398	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11854569	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11855110	0.88[EUR][1000 genomes]
rs17611465	1.00[ASN][1000 genomes]
rs1972419	1.00[ASN][1000 genomes]
rs2554354	1.00[ASN][1000 genomes]
rs2554355	1.00[ASN][1000 genomes]
rs2570243	1.00[ASN][1000 genomes]
rs2593169	1.00[ASN][1000 genomes]
rs2623245	1.00[ASN][1000 genomes]
rs2623247	1.00[ASN][1000 genomes]
rs2623251	1.00[ASN][1000 genomes]
rs2623263	1.00[ASN][1000 genomes]
rs2623270	1.00[ASN][1000 genomes]
rs28718531	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55860410	1.00[ASN][1000 genomes]
rs55922236	1.00[ASN][1000 genomes]
rs56049741	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186119	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62015208	1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]
rs8024265	1.00[ASN][1000 genomes]
rs9672830	0.81[EUR][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	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	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
4	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
5	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

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52312800-52345400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
3	chr15:52314600-52332200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:52315600-52332200	Weak transcription	NHLF	lung
5	chr15:52316000-52332200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:52317400-52332200	Weak transcription	Lung	lung
7	chr15:52321200-52332200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:52322400-52332200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:52322400-52332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:52322800-52332400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:52325800-52332000	Weak transcription	Fetal Lung	lung
12	chr15:52325800-52332200	Weak transcription	Aorta	Aorta
13	chr15:52325800-52332200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:52325800-52334200	Weak transcription	Dnd41	blood
15	chr15:52325800-52342200	Weak transcription	HUVEC	blood vessel
16	chr15:52326000-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:52326000-52332000	Weak transcription	Thymus	Thymus
18	chr15:52326000-52332200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:52326800-52342800	Weak transcription	Fetal Brain Female	brain
20	chr15:52327000-52337200	Weak transcription	Primary B cells from cord blood	blood
21	chr15:52327000-52340600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:52327200-52332200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52327400-52332000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:52327400-52332200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:52327400-52332200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:52327600-52332000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:52327600-52340200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:52328000-52333800	Enhancers	K562	blood
29	chr15:52328200-52333200	Enhancers	Liver	Liver
30	chr15:52328200-52334200	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:52328600-52332400	Weak transcription	Hela-S3	cervix
32	chr15:52329000-52332000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:52329200-52332200	Enhancers	Brain Substantia Nigra	brain
34	chr15:52329200-52333200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr15:52329400-52332200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr15:52329400-52332600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:52329400-52332800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr15:52329400-52333000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:52329400-52333000	Enhancers	Right Atrium	heart
40	chr15:52329600-52333000	Enhancers	Left Ventricle	heart
41	chr15:52329800-52332200	Enhancers	Brain Hippocampus Middle	brain
42	chr15:52329800-52333000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:52329800-52333800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:52329800-52334400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr15:52329800-52334800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr15:52330000-52332000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:52330000-52332000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:52330000-52332200	Weak transcription	Fetal Heart	heart
49	chr15:52330000-52332200	Weak transcription	GM12878-XiMat	blood
50	chr15:52330000-52332200	Weak transcription	HSMM	muscle

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