Variant report

Variant	rs17693279
Chromosome Location	chr14:39734473-39734474
allele	A/G
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	SP1	chr14:39734133-39734716	A549	lung:	n/a	n/a
2	STAT3	chr14:39734297-39734624	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr14:39733716-39734573	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr14:39734349-39734641	MCF10A-Er-Src	breast:	n/a	n/a
5	USF2	chr14:39734354-39734562	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr14:39734299-39737658	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr14:39734363-39734617	ECC-1	luminal epithelium:	n/a	chr14:39734449-39734461
8	TBP	chr14:39734305-39737329	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr14:39734303-39734615	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr14:39734387-39734679	Hela-S3	cervix:	n/a	n/a
11	FOS	chr14:39733821-39734661	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr14:39734279-39734659	Hela-S3	cervix:	n/a	chr14:39734449-39734461
13	RUNX3	chr14:39734266-39734536	GM12878	blood:	n/a	n/a
14	POLR2A	chr14:39734382-39737519	MCF10A-Er-Src	breast:	n/a	n/a
15	SP1	chr14:39734286-39734682	A549	lung:	n/a	n/a
16	STAT3	chr14:39734301-39734806	MCF10A-Er-Src	breast:	n/a	n/a
17	E2F4	chr14:39734202-39734693	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr14:39734444-39735569	K562	blood:	n/a	chr14:39735073-39735084 chr14:39734449-39734461 chr14:39735074-39735085
19	POLR2A	chr14:39734374-39734586	Hela-S3	cervix:	n/a	n/a
20	MYC	chr14:39734172-39734655	MCF10A-Er-Src	breast:	n/a	n/a
21	TAF1	chr14:39734312-39734595	Hela-S3	cervix:	n/a	n/a
22	MYC	chr14:39734215-39735841	MCF10A-Er-Src	breast:	n/a	chr14:39735299-39735308
23	POLR2A	chr14:39734322-39734608	HCT-116	colon:	n/a	n/a
24	POLR2A	chr14:39734371-39734657	Hela-S3	cervix:	n/a	n/a
25	FOS	chr14:39733768-39734608	MCF10A-Er-Src	breast:	n/a	n/a
26	SMC3	chr14:39734238-39734629	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr14:39734374-39734667	MCF-7	breast:	n/a	chr14:39734449-39734461

No.	Distal block	Cell Line	Cell type
1	chr14:39636108..39642775-chr14:39734196..39739360,12	MCF-7	breast:
2	chr14:39642546..39647225-chr14:39733415..39737853,13	MCF-7	breast:
3	chr14:39733752..39736599-chr6:27859439..27860958,2	K562	blood:
4	chr14:39570644..39573336-chr14:39733309..39737125,4	MCF-7	breast:

Variant related genes	Relation type
CTAGE5	TF binding region
ENSG00000258941	TF binding region
ENSG00000100934	Chromatin interaction
ENSG00000100941	Chromatin interaction
ENSG00000259083	Chromatin interaction
ENSG00000182400	Chromatin interaction
ENSG00000258651	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10130181	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10139591	1.00[CEU][hapmap]
rs10146622	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10148910	1.00[CEU][hapmap]
rs12433987	1.00[YRI][hapmap]
rs2415541	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2899887	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4902559	0.82[MKK][hapmap]
rs61998506	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7155173	1.00[YRI][hapmap]
rs7157316	1.00[AFR][1000 genomes]
rs8011402	0.89[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17693279	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39703600-39735400	Weak transcription	Pancreas	Pancrea
2	chr14:39728600-39735600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:39729200-39734600	Weak transcription	Fetal Intestine Small	intestine
4	chr14:39733800-39735200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr14:39734000-39735000	Enhancers	HepG2	liver
6	chr14:39734200-39735200	Enhancers	Primary hematopoietic stem cells	blood
7	chr14:39734200-39737200	Active TSS	Fetal Heart	heart
8	chr14:39734400-39734600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr14:39734400-39734600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr14:39734400-39734600	Enhancers	Fetal Brain Male	brain
11	chr14:39734400-39734600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr14:39734400-39734600	Enhancers	NHEK	skin
13	chr14:39734400-39734600	Active TSS	Osteobl	bone
14	chr14:39734400-39734800	Flanking Active TSS	Liver	Liver
15	chr14:39734400-39734800	Flanking Active TSS	Hela-S3	cervix
16	chr14:39734400-39734800	Active TSS	HMEC	breast
17	chr14:39734400-39734800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr14:39734400-39735000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:39734400-39735000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr14:39734400-39735000	Enhancers	Primary T cells from cord blood	blood
21	chr14:39734400-39735000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:39734400-39735000	Enhancers	Adipose Nuclei	Adipose
23	chr14:39734400-39735000	Enhancers	Fetal Lung	lung
24	chr14:39734400-39735000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr14:39734400-39735000	Active TSS	NH-A	brain
26	chr14:39734400-39735200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr14:39734400-39735200	Enhancers	Duodenum Mucosa	Duodenum
28	chr14:39734400-39735200	Enhancers	Dnd41	blood
29	chr14:39734400-39735200	Enhancers	NHLF	lung
30	chr14:39734400-39735400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr14:39734400-39735400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr14:39734400-39735400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr14:39734400-39735400	Enhancers	Fetal Intestine Large	intestine
34	chr14:39734400-39735600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:39734400-39735600	Flanking Active TSS	A549	lung
36	chr14:39734400-39735800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr14:39734400-39735800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr14:39734400-39736000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr14:39734400-39736000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr14:39734400-39737200	Active TSS	Fetal Stomach	stomach
41	chr14:39734400-39737400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr14:39734400-39737600	Active TSS	Brain Anterior Caudate	brain
43	chr14:39734400-39737600	Active TSS	Brain Cingulate Gyrus	brain
44	chr14:39734400-39737600	Active TSS	Fetal Muscle Leg	muscle
45	chr14:39734400-39737600	Active TSS	Right Ventricle	heart
46	chr14:39734400-39737600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr14:39734400-39737800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr14:39734400-39737800	Active TSS	Right Atrium	heart
49	chr14:39734400-39738000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:39734400-39738200	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links