Variant report

Variant	rs2440374
Chromosome Location	chr15:53097088-53097089
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ONECUT1-1	chr15:53096691-53097142	XLOC_011481
2	lnc-ONECUT1-1	chr15:53096691-53097142	XLOC_011481
3	lnc-ONECUT1-1	chr15:53096691-53097139	ENSG00000259203.1

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1814459	0.83[EUR][1000 genomes]
rs1899752	0.85[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1947043	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120442	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2165991	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243790	0.81[CHB][hapmap]
rs2244272	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2247401	0.83[EUR][1000 genomes]
rs2440315	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs2440316	0.90[EUR][1000 genomes]
rs2440349	0.83[EUR][1000 genomes]
rs2440350	0.83[EUR][1000 genomes]
rs2440352	0.95[CEU][hapmap];0.83[CHB][hapmap]
rs2440373	0.86[EUR][1000 genomes]
rs2456496	0.86[EUR][1000 genomes]
rs2456506	0.86[EUR][1000 genomes]
rs2456512	0.83[EUR][1000 genomes]
rs2456513	0.82[EUR][1000 genomes]
rs2456517	0.83[EUR][1000 genomes]
rs2456523	0.84[EUR][1000 genomes]
rs2456531	0.84[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2460	0.86[EUR][1000 genomes]
rs28687152	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7161874	0.83[EUR][1000 genomes]
rs935192	0.83[EUR][1000 genomes]
rs935194	0.81[EUR][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
4	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53095600-53097200	Bivalent Enhancer	Fetal Heart	heart
2	chr15:53095600-53097400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:53095600-53097800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr15:53095600-53098600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr15:53095600-53098800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:53095800-53097200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr15:53095800-53097200	Bivalent Enhancer	Fetal Intestine Large	intestine
8	chr15:53095800-53097200	Bivalent Enhancer	Fetal Thymus	thymus
9	chr15:53095800-53097200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
10	chr15:53095800-53097400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr15:53095800-53097400	Bivalent Enhancer	Left Ventricle	heart
12	chr15:53095800-53097800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:53095800-53097800	Active TSS	Pancreas	Pancrea
14	chr15:53095800-53097800	Bivalent/Poised TSS	Psoas Muscle	Psoas
15	chr15:53095800-53098400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr15:53095800-53098800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr15:53096000-53097200	Bivalent Enhancer	Esophagus	oesophagus
18	chr15:53096000-53097200	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr15:53096000-53098400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr15:53096000-53098400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr15:53096000-53098400	Bivalent Enhancer	Fetal Brain Male	brain
22	chr15:53096000-53098600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr15:53096000-53098600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr15:53096000-53098600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:53096200-53097800	Active TSS	Right Ventricle	heart
26	chr15:53096200-53097800	Enhancers	Spleen	Spleen
27	chr15:53096200-53098000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
28	chr15:53096200-53098000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
29	chr15:53096200-53098400	Bivalent Enhancer	Small Intestine	intestine
30	chr15:53096400-53097800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:53096400-53097800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:53096400-53098000	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr15:53096400-53098200	Active TSS	Aorta	Aorta
34	chr15:53096400-53098400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr15:53096400-53098600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:53096600-53097200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr15:53096600-53097400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
38	chr15:53096600-53097400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:53096600-53097400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
40	chr15:53096600-53097400	Flanking Active TSS	Liver	Liver
41	chr15:53096600-53097400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
42	chr15:53096600-53097600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:53096600-53098000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
44	chr15:53096600-53098200	Active TSS	H1 Cell Line	embryonic stem cell
45	chr15:53096600-53098200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:53096800-53097200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:53096800-53097200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:53096800-53097200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:53096800-53097200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr15:53096800-53097200	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood

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