Variant report

Variant	rs17109079
Chromosome Location	chr14:39735100-39735101
allele	A/C
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	EP300	chr14:39735032-39737269	HepG2	liver:	n/a	chr14:39735896-39735905 chr14:39737034-39737044 chr14:39736087-39736096 chr14:39735369-39735378 chr14:39736103-39736119
2	MXI1	chr14:39734950-39737526	GM12878	blood:	n/a	chr14:39736629-39736644 chr14:39737052-39737061 chr14:39737050-39737059
3	POLR2A	chr14:39735089-39736956	NB4	blood:	n/a	n/a
4	GTF2F1	chr14:39735010-39737329	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr14:39735034-39735350	Hela-S3	cervix:	n/a	n/a
6	REST	chr14:39735099-39737123	HL-60	blood:	n/a	chr14:39736515-39736528 chr14:39736515-39736528 chr14:39736555-39736565 chr14:39736513-39736523 chr14:39736014-39736027
7	TBP	chr14:39735063-39737219	K562	blood:	n/a	n/a
8	MBD4	chr14:39734960-39737590	HepG2	liver:	n/a	n/a
9	POLR2A	chr14:39734299-39737658	MCF10A-Er-Src	breast:	n/a	n/a
10	NFIC	chr14:39734955-39737759	HepG2	liver:	n/a	n/a
11	MAFK	chr14:39734992-39735660	K562	blood:	n/a	chr14:39735112-39735123
12	EP300	chr14:39735062-39736786	HepG2	liver:	n/a	chr14:39735896-39735905 chr14:39736087-39736096 chr14:39735369-39735378 chr14:39736103-39736119
13	MYBL2	chr14:39734846-39737218	HepG2	liver:	n/a	n/a
14	HDAC2	chr14:39735029-39737162	HepG2	liver:	n/a	chr14:39736971-39736979
15	TBP	chr14:39734305-39737329	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr14:39734861-39737343	Hela-S3	cervix:	n/a	chr14:39735073-39735084 chr14:39735074-39735085
17	POLR2A	chr14:39735074-39737302	HepG2	liver:	n/a	n/a
18	CHD1	chr14:39735032-39737962	IMR90	lung:	n/a	chr14:39736859-39736869 chr14:39736513-39736523
19	KAP1	chr14:39735053-39735861	U2OS	brain:	n/a	n/a
20	FOS	chr14:39734987-39735297	MCF10A-Er-Src	breast:	n/a	n/a
21	JUND	chr14:39735051-39735912	HepG2	liver:	n/a	chr14:39735722-39735732 chr14:39735721-39735732 chr14:39735723-39735731 chr14:39735722-39735732
22	POLR2A	chr14:39735022-39737305	GM12891	blood:	n/a	n/a
23	STAT3	chr14:39735061-39735177	MCF10A-Er-Src	breast:	n/a	chr14:39735076-39735084
24	STAT3	chr14:39734934-39735337	MCF10A-Er-Src	breast:	n/a	chr14:39735076-39735084
25	TEAD4	chr14:39734810-39738248	HepG2	liver:	n/a	n/a
26	CEBPB	chr14:39734904-39735897	A549	lung:	n/a	chr14:39735073-39735084 chr14:39735074-39735085
27	CEBPB	chr14:39734867-39735273	K562	blood:	n/a	chr14:39735073-39735084 chr14:39735074-39735085
28	FOS	chr14:39734986-39735187	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr14:39735089-39735248	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr14:39734382-39737519	MCF10A-Er-Src	breast:	n/a	n/a
31	SMC3	chr14:39735050-39737291	Hela-S3	cervix:	n/a	n/a
32	MAX	chr14:39734997-39737354	HepG2	liver:	n/a	chr14:39737051-39737060 chr14:39735299-39735308 chr14:39737049-39737062 chr14:39737050-39737060 chr14:39737050-39737061 chr14:39737046-39737065 chr14:39737050-39737061 chr14:39737052-39737061 chr14:39737049-39737059
33	STAT3	chr14:39734932-39735871	MCF10A-Er-Src	breast:	n/a	chr14:39735076-39735084
34	MAFF	chr14:39735051-39735598	K562	blood:	n/a	chr14:39735491-39735509
35	MBD4	chr14:39734959-39737377	HepG2	liver:	n/a	n/a
36	MYC	chr14:39734934-39737301	MCF10A-Er-Src	breast:	n/a	chr14:39737051-39737060 chr14:39735299-39735308 chr14:39737049-39737062 chr14:39737050-39737060 chr14:39737050-39737061 chr14:39737046-39737065 chr14:39737050-39737061 chr14:39737052-39737061 chr14:39737049-39737059
37	CEBPB	chr14:39734444-39735569	K562	blood:	n/a	chr14:39735073-39735084 chr14:39734449-39734461 chr14:39735074-39735085
38	POLR2A	chr14:39734882-39737404	HepG2	liver:	n/a	n/a
39	CEBPB	chr14:39734887-39735957	A549	lung:	n/a	chr14:39735073-39735084 chr14:39735074-39735085
40	POLR2A	chr14:39735075-39737134	Hela-S3	cervix:	n/a	n/a
41	MAFK	chr14:39734913-39735511	H1-hESC	embryonic stem cell:	n/a	chr14:39735112-39735123
42	MAFK	chr14:39734809-39738020	Hela-S3	cervix:	n/a	chr14:39736304-39736319 chr14:39737693-39737710 chr14:39737177-39737188 chr14:39735112-39735123
43	MYBL2	chr14:39734959-39737527	HepG2	liver:	n/a	n/a
44	EP300	chr14:39734512-39735759	K562	blood:	n/a	chr14:39734727-39734741 chr14:39735369-39735378
45	CEBPB	chr14:39734892-39736290	HepG2	liver:	n/a	chr14:39735073-39735084 chr14:39735074-39735085
46	FOS	chr14:39734884-39735879	MCF10A-Er-Src	breast:	n/a	chr14:39735722-39735732 chr14:39735723-39735731 chr14:39735722-39735732
47	FOS	chr14:39734935-39735886	MCF10A-Er-Src	breast:	n/a	chr14:39735722-39735732 chr14:39735723-39735731 chr14:39735722-39735732
48	MYC	chr14:39734215-39735841	MCF10A-Er-Src	breast:	n/a	chr14:39735299-39735308
49	MAFF	chr14:39735077-39735969	HepG2	liver:	n/a	chr14:39735491-39735509
50	POLR2A	chr14:39735029-39737099	Hela-S3	cervix:	n/a	n/a

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	chr14:39643730..39648156-chr14:39734640..39738499,10	MCF-7	breast:
4	chr14:39734882..39737237-chr14:39899749..39901875,2	MCF-7	breast:
5	chr14:39733752..39736599-chr6:27859439..27860958,2	K562	blood:
6	chr14:39734713..39738415-chr14:39740999..39745819,7	MCF-7	breast:
7	chr14:39680164..39682554-chr14:39734526..39737073,3	MCF-7	breast:
8	chr14:39570644..39573336-chr14:39733309..39737125,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAPPC6B-2	chr14:39734907-39736265	ENSG00000258940.2

Variant related genes	Relation type
CTAGE5	TF binding region
ENSG00000258941	TF binding region
ENSG00000150527	Chromatin interaction
ENSG00000259083	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000258671	Chromatin interaction
ENSG00000182400	Chromatin interaction
ENSG00000100941	Chromatin interaction
ENSG00000258651	Chromatin interaction
ENSG00000165355	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17108840	1.00[MEX][hapmap]
rs17108884	1.00[MEX][hapmap]
rs17108885	1.00[MEX][hapmap]
rs17108962	1.00[MEX][hapmap]
rs17108984	1.00[MEX][hapmap]
rs17109037	1.00[MEX][hapmap]
rs17109049	1.00[AMR][1000 genomes]
rs17109123	1.00[MEX][hapmap]
rs17109235	1.00[MEX][hapmap]
rs2415530	1.00[MEX][hapmap]
rs57633608	1.00[EUR][1000 genomes]
rs6571903	1.00[MEX][hapmap]
rs7144933	1.00[MEX][hapmap]
rs7150364	1.00[MEX][hapmap]
rs719456	1.00[MEX][hapmap]
rs73279345	1.00[EUR][1000 genomes]
rs8004735	1.00[EUR][1000 genomes]
rs8014741	1.00[MEX][hapmap]

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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

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	chr14:39733800-39735200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr14:39734200-39735200	Enhancers	Primary hematopoietic stem cells	blood
5	chr14:39734200-39737200	Active TSS	Fetal Heart	heart
6	chr14:39734400-39735200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr14:39734400-39735200	Enhancers	Duodenum Mucosa	Duodenum
8	chr14:39734400-39735200	Enhancers	Dnd41	blood
9	chr14:39734400-39735200	Enhancers	NHLF	lung
10	chr14:39734400-39735400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr14:39734400-39735400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr14:39734400-39735400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr14:39734400-39735400	Enhancers	Fetal Intestine Large	intestine
14	chr14:39734400-39735600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:39734400-39735600	Flanking Active TSS	A549	lung
16	chr14:39734400-39735800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr14:39734400-39735800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr14:39734400-39736000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr14:39734400-39736000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:39734400-39737200	Active TSS	Fetal Stomach	stomach
21	chr14:39734400-39737400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr14:39734400-39737600	Active TSS	Brain Anterior Caudate	brain
23	chr14:39734400-39737600	Active TSS	Brain Cingulate Gyrus	brain
24	chr14:39734400-39737600	Active TSS	Fetal Muscle Leg	muscle
25	chr14:39734400-39737600	Active TSS	Right Ventricle	heart
26	chr14:39734400-39737600	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr14:39734400-39737800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:39734400-39737800	Active TSS	Right Atrium	heart
29	chr14:39734400-39738000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr14:39734400-39738200	Active TSS	Aorta	Aorta
31	chr14:39734600-39735200	Enhancers	Primary B cells from cord blood	blood
32	chr14:39734600-39735200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr14:39734600-39735200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr14:39734600-39735400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr14:39734600-39735400	Enhancers	Fetal Intestine Small	intestine
36	chr14:39734600-39735600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr14:39734600-39735600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr14:39734600-39735600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr14:39734600-39735800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:39734600-39735800	Flanking Active TSS	NHEK	skin
41	chr14:39734600-39735800	Flanking Active TSS	Osteobl	bone
42	chr14:39734600-39737200	Active TSS	Fetal Kidney	kidney
43	chr14:39734600-39737400	Active TSS	Brain Substantia Nigra	brain
44	chr14:39734600-39737600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr14:39734600-39737600	Active TSS	Brain Hippocampus Middle	brain
46	chr14:39734600-39738200	Active TSS	HSMMtube	muscle
47	chr14:39734600-39738800	Active TSS	Psoas Muscle	Psoas
48	chr14:39734800-39735200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr14:39734800-39735200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr14:39734800-39735800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links