Variant report

Variant	rs60253448
Chromosome Location	chr13:93877328-93877329
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	TEAD4	chr13:93876578-93877341	HepG2	liver:	n/a	chr13:93876920-93876929
2	FOXA1	chr13:93876652-93877329	HepG2	liver:	n/a	n/a
3	NR2F2	chr13:93876738-93877336	MCF-7	breast:	n/a	n/a
4	MYBL2	chr13:93876649-93877343	HepG2	liver:	n/a	n/a
5	EP300	chr13:93876657-93877366	MCF-7	breast:	n/a	n/a
6	JUND	chr13:93876776-93877455	HepG2	liver:	n/a	chr13:93877371-93877381 chr13:93877067-93877076
7	EP300	chr13:93876586-93877335	A549	lung:	n/a	n/a
8	MAFK	chr13:93876907-93877720	HepG2	liver:	n/a	chr13:93877370-93877380
9	JUN	chr13:93876817-93877454	HepG2	liver:	n/a	chr13:93877371-93877381 chr13:93877067-93877076
10	CEBPB	chr13:93876714-93877376	A549	lung:	n/a	n/a
11	STAT5A	chr13:93877250-93877614	K562	blood:	n/a	chr13:93877490-93877497
12	MAFK	chr13:93876820-93877446	HepG2	liver:	n/a	chr13:93877370-93877380
13	FOXM1	chr13:93876659-93877357	MCF-7	breast:	n/a	n/a
14	EP300	chr13:93876553-93877525	A549	lung:	n/a	chr13:93877417-93877430
15	SP1	chr13:93876570-93877358	A549	lung:	n/a	n/a
16	NR2F2	chr13:93876670-93877426	HepG2	liver:	n/a	n/a
17	GATA3	chr13:93876641-93877431	MCF-7	breast:	n/a	n/a
18	EP300	chr13:93876798-93877453	HepG2	liver:	n/a	chr13:93877417-93877430
19	TCF12	chr13:93876562-93877344	A549	lung:	n/a	n/a
20	ARID3A	chr13:93876694-93877378	HepG2	liver:	n/a	n/a

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:

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

Variant related genes	Relation type
GPC6	TF binding region

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs73540341	1.00[AMR][1000 genomes]
rs73540354	1.00[AMR][1000 genomes]
rs73554228	1.00[AMR][1000 genomes]
rs73628654	1.00[AMR][1000 genomes]
rs73628694	1.00[AMR][1000 genomes]
rs73628695	1.00[AMR][1000 genomes]
rs74108506	1.00[AMR][1000 genomes]
rs74108508	1.00[AMR][1000 genomes]
rs74108509	1.00[AMR][1000 genomes]
rs7986020	1.00[AMR][1000 genomes]
rs8001040	1.00[AMR][1000 genomes]
rs9584109	1.00[AMR][1000 genomes]
rs9589718	1.00[AMR][1000 genomes]
rs9589719	1.00[AMR][1000 genomes]
rs9589723	1.00[AMR][1000 genomes]
rs9589725	1.00[AMR][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:51 , 50 per page) page: 1 2

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	chr13:93876600-93877600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr13:93876600-93877600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:93876600-93877600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr13:93876600-93877600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr13:93876600-93878000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr13:93876600-93878000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:93876600-93878200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr13:93876600-93878400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:93876600-93878400	Enhancers	Fetal Intestine Small	intestine
21	chr13:93876600-93878600	Weak transcription	NHDF-Ad	bronchial
22	chr13:93876600-93878800	Flanking Active TSS	Liver	Liver
23	chr13:93876800-93877400	Enhancers	Fetal Lung	lung
24	chr13:93876800-93877400	Enhancers	Osteobl	bone
25	chr13:93876800-93877600	Enhancers	Fetal Heart	heart
26	chr13:93876800-93878000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:93876800-93878200	Enhancers	NH-A	brain
28	chr13:93876800-93878400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:93876800-93878400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:93876800-93878400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr13:93876800-93878400	Enhancers	Fetal Intestine Large	intestine
32	chr13:93876800-93878600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr13:93876800-93878600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:93876800-93879000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:93876800-93879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr13:93877000-93877400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr13:93877000-93877600	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr13:93877000-93877800	Weak transcription	HMEC	breast
39	chr13:93877000-93878200	Weak transcription	HSMM	muscle
40	chr13:93877000-93878400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:93877000-93878400	Enhancers	HSMMtube	muscle
42	chr13:93877000-93878800	Flanking Active TSS	HepG2	liver
43	chr13:93877000-93879200	Active TSS	A549	lung
44	chr13:93877200-93877600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr13:93877200-93877600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:93877200-93877600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:93877200-93878000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr13:93877200-93878200	Enhancers	Adipose Nuclei	Adipose
49	chr13:93877200-93878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:93877200-93878400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links