Variant report

Variant	rs28661826
Chromosome Location	chr15:43018559-43018560
allele	C/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	chr15:43018379-43018987	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:43018403-43018845	K562	blood:	n/a	n/a
3	CTCF	chr15:43018440-43018590	K562	blood:	n/a	chr15:43018481-43018490
4	CTCF	chr15:43018420-43018570	Hela-S3	cervix:	n/a	chr15:43018481-43018490
5	POLR2A	chr15:43018537-43019064	K562	blood:	n/a	n/a
6	POLR2A	chr15:43018548-43019893	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr15:43018534-43019119	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr15:43018489-43018622	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43014319..43018768-chr15:43027782..43030873,5	MCF-7	breast:

Variant related genes	Relation type
CDAN1	TF binding region
ENSG00000140326	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11632809	0.85[AFR][1000 genomes]
rs12323990	0.98[ASN][1000 genomes]
rs12591415	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12592374	1.00[ASN][1000 genomes]
rs12592573	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594325	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594378	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12594600	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594696	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594699	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12594724	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594725	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594765	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12594837	0.98[ASN][1000 genomes]
rs12595722	0.83[ASN][1000 genomes]
rs16957055	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16957061	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16957063	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16957120	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28431056	1.00[ASN][1000 genomes]
rs28437884	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28542286	0.86[AFR][1000 genomes]
rs28680600	0.95[ASN][1000 genomes]
rs34302400	0.85[AFR][1000 genomes]
rs3742992	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3742995	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4334272	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56046122	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58237318	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs58548142	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs60723187	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61747153	0.98[ASN][1000 genomes]
rs7169231	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7169238	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7181238	0.84[AFR][1000 genomes]
rs73410923	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73410927	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410931	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410937	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410940	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410959	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410961	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410969	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410971	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410972	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410973	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8028365	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8028699	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8033336	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8036733	0.98[ASN][1000 genomes]
rs8042980	0.82[AFR][1000 genomes]
rs9920562	0.85[AFR][1000 genomes]

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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers 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	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS 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	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43000800-43018600	Weak transcription	A549	lung
2	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
3	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
9	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
10	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
13	chr15:43008800-43027200	Strong transcription	Lung	lung
14	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
15	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
19	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
21	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine
22	chr15:43009600-43027800	Strong transcription	Left Ventricle	heart
23	chr15:43009800-43018600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:43009800-43020800	Weak transcription	Stomach Mucosa	stomach
25	chr15:43010000-43020200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:43010000-43027200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:43010000-43027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:43010000-43027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:43010000-43027600	Strong transcription	Brain Anterior Caudate	brain
30	chr15:43010000-43027600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr15:43010200-43027400	Strong transcription	Primary T cells from cord blood	blood
32	chr15:43010200-43027600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:43010200-43027600	Strong transcription	Ovary	ovary
34	chr15:43010200-43027800	Strong transcription	Gastric	stomach
35	chr15:43010400-43026800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr15:43010400-43026800	Strong transcription	Thymus	Thymus
37	chr15:43010400-43027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:43010400-43027800	Strong transcription	Placenta	Placenta
39	chr15:43010800-43020600	Strong transcription	Fetal Lung	lung
40	chr15:43011000-43026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:43011000-43026800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:43011000-43027200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:43011200-43020400	Strong transcription	Primary B cells from cord blood	blood
44	chr15:43011200-43027600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr15:43011400-43027600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:43011600-43019800	Weak transcription	Fetal Heart	heart
47	chr15:43011600-43022800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:43011600-43028000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:43011800-43026400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:43011800-43027000	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links