Variant report

Variant	rs17702471
Chromosome Location	chr13:93877117-93877118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:112)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:112 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr13:93876672-93877198	A549	lung:	n/a	n/a
2	MBD4	chr13:93876705-93877278	HepG2	liver:	n/a	n/a
3	TEAD4	chr13:93876659-93877206	A549	lung:	n/a	chr13:93876920-93876929
4	CEBPB	chr13:93876880-93877153	HepG2	liver:	n/a	n/a
5	TEAD4	chr13:93876578-93877341	HepG2	liver:	n/a	chr13:93876920-93876929
6	HDAC2	chr13:93876763-93877268	MCF-7	breast:	n/a	n/a
7	FOXA1	chr13:93876652-93877329	HepG2	liver:	n/a	n/a
8	NR2F2	chr13:93876738-93877336	MCF-7	breast:	n/a	n/a
9	MBD4	chr13:93876658-93877265	HepG2	liver:	n/a	n/a
10	EP300	chr13:93876717-93877264	HepG2	liver:	n/a	n/a
11	MAFF	chr13:93876859-93877246	HepG2	liver:	n/a	n/a
12	ATF2	chr13:93876719-93877162	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr13:93876780-93877201	HepG2	liver:	n/a	n/a
14	NR3C1	chr13:93876817-93877120	A549	lung:	n/a	n/a
15	MAX	chr13:93876695-93877292	HepG2	liver:	n/a	n/a
16	RCOR1	chr13:93876772-93877179	HepG2	liver:	n/a	n/a
17	HDAC2	chr13:93876836-93877153	H1-hESC	embryonic stem cell:	n/a	n/a
18	RFX5	chr13:93876832-93877133	HepG2	liver:	n/a	n/a
19	ESR1	chr13:93876724-93877219	T-47D	breast:	n/a	n/a
20	MYBL2	chr13:93876649-93877343	HepG2	liver:	n/a	n/a
21	HNF4A	chr13:93876787-93877178	HepG2	liver:	n/a	n/a
22	REST	chr13:93876795-93877138	HepG2	liver:	n/a	n/a
23	ESR1	chr13:93876810-93877148	T-47D	breast:	n/a	n/a
24	EP300	chr13:93876826-93877238	MCF-7	breast:	n/a	n/a
25	HNF4G	chr13:93876714-93877195	HepG2	liver:	n/a	chr13:93876987-93877002
26	TCF12	chr13:93876813-93877181	HepG2	liver:	n/a	n/a
27	FOXA2	chr13:93876743-93877205	HepG2	liver:	n/a	n/a
28	TCF12	chr13:93876777-93877184	A549	lung:	n/a	n/a
29	FOSL2	chr13:93876726-93877233	HepG2	liver:	n/a	chr13:93877067-93877076
30	RAD21	chr13:93876795-93877124	HepG2	liver:	n/a	n/a
31	KAP1	chr13:93876832-93877208	U2OS	brain:	n/a	n/a
32	FOSL2	chr13:93876748-93877130	HepG2	liver:	n/a	chr13:93877067-93877076
33	CEBPB	chr13:93876856-93877195	A549	lung:	n/a	n/a
34	SP1	chr13:93876640-93877209	HepG2	liver:	n/a	n/a
35	CEBPB	chr13:93876787-93877286	MCF-7	breast:	n/a	n/a
36	EP300	chr13:93876642-93877294	HepG2	liver:	n/a	n/a
37	HDAC2	chr13:93876678-93877226	HepG2	liver:	n/a	n/a
38	EP300	chr13:93876657-93877366	MCF-7	breast:	n/a	n/a
39	JUND	chr13:93876776-93877455	HepG2	liver:	n/a	chr13:93877371-93877381 chr13:93877067-93877076
40	EP300	chr13:93876586-93877335	A549	lung:	n/a	n/a
41	NR3C1	chr13:93876811-93877118	A549	lung:	n/a	n/a
42	FOXA1	chr13:93876642-93877314	HepG2	liver:	n/a	n/a
43	GABPA	chr13:93876789-93877264	MCF-7	breast:	n/a	n/a
44	CEBPB	chr13:93876804-93877250	HepG2	liver:	n/a	n/a
45	CEBPB	chr13:93876828-93877277	MCF-7	breast:	n/a	n/a
46	CEBPB	chr13:93876779-93877167	HepG2	liver:	n/a	n/a
47	MAFK	chr13:93876907-93877720	HepG2	liver:	n/a	chr13:93877370-93877380
48	MAZ	chr13:93876897-93877146	HepG2	liver:	n/a	n/a
49	CEBPZ	chr13:93876795-93877284	HepG2	liver:	n/a	n/a
50	TEAD4	chr13:93876576-93877187	A549	lung:	n/a	chr13:93876920-93876929

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:93875719..93877813-chr13:93914572..93917548,2	K562	blood:
2	chr13:93876590..93877329-chr13:93885822..93886900,3	MCF-7	breast:
3	chr13:93876570..93877337-chr13:93886214..93886903,5	MCF-7	breast:
4	chr13:93876646..93877175-chr13:93885988..93886813,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCT-16	chr13:93876780-93879077	NONHSAT034710

No data

Variant related genes	Relation type
GPC6	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1328366	0.83[GIH][hapmap]
rs1328370	1.00[ASW][hapmap];0.84[TSI][hapmap]
rs17267523	1.00[LWK][hapmap];0.83[TSI][hapmap]
rs17645969	0.84[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17645998	0.84[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2004191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2209880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400921	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61963718	0.85[EUR][1000 genomes]
rs72633947	0.85[EUR][1000 genomes]
rs8181846	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561275	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9561276	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561281	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93869000-93878200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:93871200-93877800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:93871200-93878400	Weak transcription	Fetal Brain Female	brain
4	chr13:93874800-93878200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:93875000-93878200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr13:93875400-93877400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr13:93875400-93878200	Weak transcription	Right Atrium	heart
8	chr13:93875600-93878000	Weak transcription	Brain Germinal Matrix	brain
9	chr13:93875600-93878200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr13:93875800-93878400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:93876000-93878000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr13:93876600-93877200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:93876600-93877200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr13:93876600-93877600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr13:93876600-93877600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:93876600-93877600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr13:93876600-93877600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr13:93876600-93878000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr13:93876600-93878000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr13:93876600-93878200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr13:93876600-93878400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr13:93876600-93878400	Enhancers	Fetal Intestine Small	intestine
23	chr13:93876600-93878600	Weak transcription	NHDF-Ad	bronchial
24	chr13:93876600-93878800	Flanking Active TSS	Liver	Liver
25	chr13:93876800-93877200	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr13:93876800-93877200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr13:93876800-93877200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr13:93876800-93877200	Enhancers	Fetal Kidney	kidney
29	chr13:93876800-93877400	Enhancers	Fetal Lung	lung
30	chr13:93876800-93877400	Enhancers	Osteobl	bone
31	chr13:93876800-93877600	Enhancers	Fetal Heart	heart
32	chr13:93876800-93878000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:93876800-93878200	Enhancers	NH-A	brain
34	chr13:93876800-93878400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:93876800-93878400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:93876800-93878400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr13:93876800-93878400	Enhancers	Fetal Intestine Large	intestine
38	chr13:93876800-93878600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr13:93876800-93878600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:93876800-93879000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:93876800-93879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr13:93877000-93877400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr13:93877000-93877600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr13:93877000-93877800	Weak transcription	HMEC	breast
45	chr13:93877000-93878200	Weak transcription	HSMM	muscle
46	chr13:93877000-93878400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr13:93877000-93878400	Enhancers	HSMMtube	muscle
48	chr13:93877000-93878800	Flanking Active TSS	HepG2	liver
49	chr13:93877000-93879200	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links