Variant report

Variant	rs34789145
Chromosome Location	chr17:38471325-38471326
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	chr17:38470275-38471462	A549	lung:	n/a	chr17:38470750-38470764 chr17:38470699-38470713 chr17:38470831-38470845 chr17:38470630-38470644 chr17:38470635-38470644
2	TEAD4	chr17:38470624-38471345	A549	lung:	n/a	n/a
3	TCF12	chr17:38470496-38471355	A549	lung:	n/a	chr17:38470709-38470719
4	GATA3	chr17:38470609-38471374	MCF-7	breast:	n/a	n/a
5	POLR2A	chr17:38470493-38471359	PANC-1	pancreas:	n/a	n/a
6	MAX	chr17:38469457-38471385	A549	lung:	n/a	n/a
7	HDAC2	chr17:38470823-38471356	MCF-7	breast:	n/a	n/a
8	JUND	chr17:38470650-38471372	MCF-7	breast:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471036-38471047 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471071-38471082 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
9	TEAD4	chr17:38470739-38471350	ECC-1	luminal epithelium:	n/a	n/a
10	TCF7L2	chr17:38470873-38471328	HCT-116	colon:	n/a	chr17:38471038-38471047 chr17:38471037-38471046 chr17:38471073-38471082
11	EP300	chr17:38470007-38471505	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr17:38470683-38471377	MCF-7	breast:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38470975-38470986 chr17:38471037-38471048 chr17:38471073-38471081
13	ATF3	chr17:38470473-38471335	A549	lung:	n/a	n/a
14	TEAD4	chr17:38470680-38471376	HCT-116	colon:	n/a	n/a
15	EP300	chr17:38470260-38471352	ECC-1	luminal epithelium:	n/a	n/a
16	JUND	chr17:38470480-38471834	HCT-116	colon:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471036-38471047 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471071-38471082 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
17	TCF12	chr17:38470316-38471570	ECC-1	luminal epithelium:	n/a	chr17:38470709-38470719
18	NFIC	chr17:38469944-38471393	SK-N-SH	brain:	n/a	chr17:38470783-38470811
19	EP300	chr17:38470512-38471341	MCF-7	breast:	n/a	n/a
20	FOSL1	chr17:38470506-38471537	HCT-116	colon:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
21	SP1	chr17:38470405-38471362	HCT-116	colon:	n/a	chr17:38470750-38470764 chr17:38470699-38470713 chr17:38470831-38470845 chr17:38470630-38470644 chr17:38470635-38470644
22	MAZ	chr17:38470557-38471358	IMR90	lung:	n/a	n/a
23	MAX	chr17:38470463-38471357	ECC-1	luminal epithelium:	n/a	n/a
24	EP300	chr17:38470553-38471383	SK-N-SH	brain:	n/a	n/a
25	NFIC	chr17:38470276-38471382	ECC-1	luminal epithelium:	n/a	chr17:38470783-38470811
26	JUND	chr17:38470450-38471366	SK-N-SH	brain:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471036-38471047 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471071-38471082 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
27	SP1	chr17:38470124-38471520	HCT-116	colon:	n/a	chr17:38470750-38470764 chr17:38470699-38470713 chr17:38470831-38470845 chr17:38470630-38470644 chr17:38470635-38470644
28	ZBTB7A	chr17:38470268-38471347	ECC-1	luminal epithelium:	n/a	chr17:38470894-38470903
29	CEBPB	chr17:38470711-38471339	A549	lung:	n/a	n/a
30	SMARCC1	chr17:38470640-38471337	Hela-S3	cervix:	n/a	chr17:38471073-38471082 chr17:38471037-38471046
31	GABPA	chr17:38470738-38471331	A549	lung:	n/a	n/a
32	GATA3	chr17:38470424-38471352	A549	lung:	n/a	n/a
33	FOSL2	chr17:38469714-38471513	A549	lung:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38470975-38470986 chr17:38471037-38471048 chr17:38471073-38471081
34	JUND	chr17:38470146-38471340	A549	lung:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471036-38471047 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471071-38471082 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
35	MAX	chr17:38470442-38471365	A549	lung:	n/a	n/a
36	SIN3AK20	chr17:38470557-38471335	MCF-7	breast:	n/a	n/a
37	TEAD4	chr17:38470687-38471332	SK-N-SH	brain:	n/a	n/a
38	JUN	chr17:38470788-38471344	K562	blood:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
39	GATA3	chr17:38470597-38471491	MCF-7	breast:	n/a	n/a
40	FOS	chr17:38470835-38471504	MCF10A-Er-Src	breast:	n/a	chr17:38471036-38471047 chr17:38471071-38471082 chr17:38470977-38470987 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
41	MAX	chr17:38470684-38471343	SK-N-SH	brain:	n/a	n/a
42	JUND	chr17:38470106-38471359	SK-N-SH	brain:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471036-38471047 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471071-38471082 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
43	TCF12	chr17:38470005-38471414	SK-N-SH	brain:	n/a	chr17:38470709-38470719
44	MAX	chr17:38470483-38471344	ECC-1	luminal epithelium:	n/a	n/a
45	TCF12	chr17:38469970-38471566	SK-N-SH	brain:	n/a	chr17:38470709-38470719
46	POLR2A	chr17:38470738-38471339	HCT-116	colon:	n/a	n/a
47	FOSL2	chr17:38470631-38471366	SK-N-SH	brain:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38470975-38470986 chr17:38471037-38471048 chr17:38471073-38471081
48	FOSL1	chr17:38470665-38471328	HCT-116	colon:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38470728-38470736 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
49	JUND	chr17:38470850-38471327	T-47D	breast:	n/a	chr17:38470977-38470987 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38471036-38471047 chr17:38471071-38471083 chr17:38471037-38471046 chr17:38471071-38471082 chr17:38471072-38471082 chr17:38470977-38470987 chr17:38471072-38471082 chr17:38470981-38470991 chr17:38470977-38470987 chr17:38471073-38471081
50	EGR1	chr17:38470502-38471394	HCT-116	colon:	n/a	chr17:38470749-38470762 chr17:38470629-38470642 chr17:38470826-38470848 chr17:38470830-38470843 chr17:38471118-38471131 chr17:38470830-38470843 chr17:38470752-38470762 chr17:38470812-38470825 chr17:38470632-38470642

No.	Distal block	Cell Line	Cell type
1	chr17:38331383..38339312-chr17:38470464..38480799,28	MCF-7	breast:
2	chr17:38470862..38473621-chr17:38773618..38775413,2	MCF-7	breast:
3	chr17:38470849..38471379-chr17:38478387..38478891,2	MCF-7	breast:
4	chr17:38257297..38260164-chr17:38470426..38472629,2	MCF-7	breast:
5	chr17:38469740..38472162-chr17:38487201..38489333,2	K562	blood:
6	chr17:38470465..38471436-chr17:38604585..38605509,3	MCF-7	breast:
7	chr17:38467971..38471563-chr17:39690230..39693084,3	MCF-7	breast:
8	chr17:37895817..37898083-chr17:38469749..38471767,2	MCF-7	breast:
9	chr17:38255744..38258787-chr17:38469945..38472055,3	MCF-7	breast:
10	chr17:38470665..38472653-chr17:39676662..39678450,2	MCF-7	breast:
11	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:
12	chr17:38445598..38447328-chr17:38470117..38471980,2	MCF-7	breast:
13	chr17:38470465..38471386-chr17:38604585..38605468,3	MCF-7	breast:
14	chr17:38470814..38471349-chr17:38478334..38478891,2	MCF-7	breast:
15	chr17:38464338..38472007-chr17:38495904..38503617,17	K562	blood:

Variant related genes	Relation type
RARA	TF binding region
ENSG00000108352	Chromatin interaction
ENSG00000265666	Chromatin interaction
ENSG00000171346	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000141753	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1130199	0.92[ASW][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12936565	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12937995	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12944531	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12947188	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7213066	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7218938	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7224658	1.00[ASW][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8065665	1.00[ASW][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8066144	0.83[LWK][hapmap];0.91[MKK][hapmap]
rs8067148	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8072718	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8074251	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8076915	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9892367	0.92[ASW][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1825614	chr17:38466377-38481100	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1063310	chr17:38467043-38499351	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1057471	chr17:38467043-38502453	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34789145	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr17:38462200-38473200	Enhancers	NHDF-Ad	bronchial
3	chr17:38462600-38474000	Enhancers	Lung	lung
4	chr17:38462800-38473000	Enhancers	Psoas Muscle	Psoas
5	chr17:38465600-38473200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:38465800-38472800	Enhancers	Esophagus	oesophagus
7	chr17:38465800-38473000	Enhancers	Placenta	Placenta
8	chr17:38465800-38473000	Enhancers	Right Ventricle	heart
9	chr17:38465800-38473400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr17:38465800-38473800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr17:38465800-38474000	Enhancers	Spleen	Spleen
12	chr17:38466000-38471800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:38466000-38471800	Enhancers	Gastric	stomach
14	chr17:38466000-38472400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:38466000-38472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:38466000-38472600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:38466000-38472600	Enhancers	HMEC	breast
18	chr17:38466000-38473000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:38466000-38473000	Enhancers	Left Ventricle	heart
20	chr17:38466000-38473800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr17:38466200-38471400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr17:38466200-38471400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:38466200-38471400	Enhancers	Liver	Liver
24	chr17:38466200-38471600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:38466200-38471800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr17:38466200-38471800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:38466200-38472000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:38466200-38472200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr17:38466200-38472600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:38466200-38473000	Enhancers	Fetal Muscle Leg	muscle
31	chr17:38466200-38473400	Enhancers	Pancreas	Pancrea
32	chr17:38466200-38473600	Enhancers	Primary hematopoietic stem cells	blood
33	chr17:38466200-38473800	Enhancers	Fetal Thymus	thymus
34	chr17:38466400-38471400	Enhancers	Right Atrium	heart
35	chr17:38466400-38472600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr17:38466400-38472600	Enhancers	Adipose Nuclei	Adipose
37	chr17:38466400-38473400	Enhancers	Stomach Mucosa	stomach
38	chr17:38466400-38474000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:38466400-38474000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr17:38466600-38472600	Enhancers	NHEK	skin
41	chr17:38466600-38472800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr17:38466600-38472800	Enhancers	Fetal Muscle Trunk	muscle
43	chr17:38466600-38473000	Enhancers	Fetal Stomach	stomach
44	chr17:38466800-38473800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr17:38466800-38473800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr17:38466800-38474000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr17:38467200-38472400	Enhancers	Fetal Lung	lung
48	chr17:38467200-38473000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr17:38467200-38473000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr17:38467200-38473200	Enhancers	HUVEC	blood vessel

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