Variant report

Variant	rs2252366
Chromosome Location	chr15:57588753-57588754
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	CTCF	chr15:57588700-57588850	HFF-Myc	foreskin:	n/a	n/a
2	CEBPB	chr15:57588631-57588941	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:57588741-57588923	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:57588124-57589126	K562	blood:	n/a	n/a
5	CTCF	chr15:57588676-57588984	H1-hESC	embryonic stem cell:	n/a	chr15:57588848-57588861
6	POLR2A	chr15:57588203-57590087	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57582041..57585604-chr15:57586782..57591985,5	K562	blood:
2	chr15:57588417..57590307-chr15:57592744..57595404,2	K562	blood:

Variant related genes	Relation type
LINC00926	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2245616	1.00[YRI][hapmap]
rs2544128	1.00[YRI][hapmap]
rs2591073	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2593245	1.00[YRI][hapmap]
rs2593253	1.00[YRI][hapmap]
rs2615234	1.00[YRI][hapmap]
rs2615239	1.00[YRI][hapmap]
rs2703585	1.00[YRI][hapmap]
rs2703617	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
2	chr15:57566000-57591600	Weak transcription	Esophagus	oesophagus
3	chr15:57568000-57590600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:57568200-57591600	Weak transcription	Psoas Muscle	Psoas
5	chr15:57573800-57589000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:57575000-57589200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:57578200-57589200	Weak transcription	Pancreas	Pancrea
8	chr15:57578600-57591600	Weak transcription	Spleen	Spleen
9	chr15:57578600-57598200	Weak transcription	Right Ventricle	heart
10	chr15:57578800-57592800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:57579200-57589600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:57579200-57592800	Weak transcription	Small Intestine	intestine
13	chr15:57579600-57589200	Weak transcription	Brain Substantia Nigra	brain
14	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:57579800-57588800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:57579800-57589200	Weak transcription	Brain Anterior Caudate	brain
17	chr15:57579800-57590400	Weak transcription	Brain Angular Gyrus	brain
18	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
21	chr15:57580000-57598400	Weak transcription	NHEK	skin
22	chr15:57580200-57589000	Weak transcription	Fetal Brain Female	brain
23	chr15:57580200-57589200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:57580400-57588800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:57580400-57589200	Weak transcription	HMEC	breast
26	chr15:57580600-57594800	Weak transcription	HepG2	liver
27	chr15:57580800-57589000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:57581000-57591600	Weak transcription	NHLF	lung
29	chr15:57581200-57591000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:57581400-57590800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr15:57581600-57595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:57581800-57590600	Weak transcription	NH-A	brain
33	chr15:57583200-57591600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr15:57583200-57591800	Weak transcription	Placenta	Placenta
35	chr15:57583400-57588800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:57583400-57589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:57583400-57590600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:57583400-57595000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
40	chr15:57583600-57589600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:57583600-57590400	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:57583600-57590400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:57583600-57598000	Weak transcription	Liver	Liver
44	chr15:57583600-57598200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:57583600-57598400	Weak transcription	A549	lung
46	chr15:57583800-57589000	Weak transcription	Primary B cells from cord blood	blood
47	chr15:57583800-57590000	Weak transcription	Fetal Kidney	kidney
48	chr15:57583800-57590400	Weak transcription	Fetal Lung	lung
49	chr15:57583800-57591000	Weak transcription	Ovary	ovary
50	chr15:57583800-57595400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links