Variant report

Variant	rs12913170
Chromosome Location	chr15:40376208-40376209
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	FOXA1	chr15:40375909-40376242	HepG2	liver:	n/a	n/a
2	CEBPB	chr15:40375979-40376259	HepG2	liver:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
3	EP300	chr15:40375854-40376255	HepG2	liver:	n/a	chr15:40376121-40376135
4	MXI1	chr15:40375960-40376277	HepG2	liver:	n/a	n/a
5	MYC	chr15:40375933-40376323	NB4	blood:	n/a	n/a
6	CEBPB	chr15:40375979-40376243	HepG2	liver:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
7	CEBPD	chr15:40375996-40376260	HepG2	liver:	n/a	chr15:40376121-40376132
8	FOXA1	chr15:40375819-40376294	HepG2	liver:	n/a	n/a
9	RXRA	chr15:40375943-40376249	HepG2	liver:	n/a	n/a
10	FOXA1	chr15:40375924-40376323	HepG2	liver:	n/a	n/a
11	MAFF	chr15:40376015-40376215	HepG2	liver:	n/a	n/a
12	CEBPB	chr15:40376016-40376263	Hela-S3	cervix:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
13	USF2	chr15:40376060-40376258	HepG2	liver:	n/a	n/a
14	MAX	chr15:40375817-40376414	HepG2	liver:	n/a	n/a
15	MAX	chr15:40375933-40376313	NB4	blood:	n/a	n/a
16	CEBPB	chr15:40375954-40376306	HepG2	liver:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
17	CEBPB	chr15:40375947-40376313	HepG2	liver:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
18	BHLHE40	chr15:40375934-40376286	HepG2	liver:	n/a	n/a
19	FOXA2	chr15:40375942-40376278	HepG2	liver:	n/a	n/a
20	CEBPB	chr15:40375953-40376314	IMR90	lung:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
21	CEBPB	chr15:40375988-40376267	K562	blood:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
22	MAX	chr15:40375992-40376239	HepG2	liver:	n/a	n/a
23	USF1	chr15:40376044-40376211	HepG2	liver:	n/a	n/a
24	CEBPB	chr15:40375974-40376292	K562	blood:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
25	SMC3	chr15:40376011-40376211	HepG2	liver:	n/a	n/a
26	FOXA1	chr15:40375934-40376340	HepG2	liver:	n/a	n/a
27	CEBPD	chr15:40376015-40376221	HepG2	liver:	n/a	chr15:40376121-40376132
28	ARID3A	chr15:40375973-40376245	HepG2	liver:	n/a	n/a
29	EP300	chr15:40375890-40376280	HepG2	liver:	n/a	chr15:40376121-40376135
30	CEBPB	chr15:40375986-40376211	MCF-7	breast:	n/a	chr15:40376120-40376131 chr15:40376120-40376133
31	EP300	chr15:40376021-40376250	HepG2	liver:	n/a	chr15:40376121-40376135

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40371046..40373186-chr15:40375916..40377601,2	MCF-7	breast:
2	chr15:40375380..40377827-chr15:40379626..40381482,2	K562	blood:

Variant related genes	Relation type
ENSG00000259409	TF binding region
ENSG00000259409	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10518679	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12050884	1.00[CHB][hapmap]
rs12899662	0.80[EUR][1000 genomes]
rs17723097	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12913170	AVEN	cis	cerebellum	SCAN
rs12913170	SRP14-AS1	cis	lung	GTEx
rs12913170	NOP10	cis	cerebellum	SCAN
rs12913170	SPRED1	cis	parietal	SCAN
rs12913170	SRP14	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40364800-40376800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:40372400-40376400	Enhancers	Fetal Heart	heart
3	chr15:40372800-40377000	Enhancers	Hela-S3	cervix
4	chr15:40373000-40376400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr15:40373800-40378800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:40374000-40376600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:40374200-40376400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:40374200-40381400	Enhancers	Fetal Thymus	thymus
9	chr15:40374200-40388200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:40374400-40376400	Enhancers	Primary B cells from cord blood	blood
11	chr15:40374400-40376400	Enhancers	Fetal Lung	lung
12	chr15:40374400-40377800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:40374400-40379000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:40374600-40376400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:40374600-40377800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:40374600-40377800	Enhancers	Primary T cells from cord blood	blood
17	chr15:40374600-40379200	Weak transcription	Aorta	Aorta
18	chr15:40374800-40376800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:40374800-40377000	Weak transcription	NH-A	brain
20	chr15:40374800-40377600	Enhancers	Primary B cells from peripheral blood	blood
21	chr15:40374800-40377600	Enhancers	Thymus	Thymus
22	chr15:40374800-40377600	Weak transcription	HMEC	breast
23	chr15:40374800-40379400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:40374800-40380400	Weak transcription	Ovary	ovary
25	chr15:40374800-40380600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:40374800-40382000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:40374800-40383800	Weak transcription	Brain Substantia Nigra	brain
28	chr15:40375000-40376400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr15:40375000-40376600	Enhancers	Liver	Liver
30	chr15:40375000-40376800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:40375000-40377400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:40375000-40377400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:40375000-40378600	Weak transcription	Psoas Muscle	Psoas
34	chr15:40375000-40378800	Weak transcription	Right Atrium	heart
35	chr15:40375000-40378800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:40375000-40379200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:40375000-40380800	Weak transcription	NHLF	lung
38	chr15:40375000-40382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:40375000-40383600	Weak transcription	Brain Anterior Caudate	brain
40	chr15:40375000-40383800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:40375000-40384200	Weak transcription	Brain Angular Gyrus	brain
42	chr15:40375200-40377000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:40375200-40377400	Weak transcription	Right Ventricle	heart
44	chr15:40375200-40378400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:40375200-40378800	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:40375200-40378800	Weak transcription	Pancreas	Pancrea
47	chr15:40375200-40378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:40375200-40378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:40375200-40379000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:40375200-40380800	Weak transcription	Primary monocytes fromperipheralblood	blood

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