Variant report

Variant	rs3809325
Chromosome Location	chr13:50266109-50266110
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	CEBPB	chr13:50265502-50266142	HCT-116	colon:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
2	MYC	chr13:50264807-50266122	MCF10A-Er-Src	breast:	n/a	chr13:50266048-50266058
3	MAX	chr13:50264970-50266242	A549	lung:	n/a	chr13:50266048-50266058
4	CEBPB	chr13:50265611-50266135	MCF-7	breast:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
5	POLR2A	chr13:50264906-50266121	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr13:50265211-50266114	MCF-7	breast:	n/a	n/a
7	POLR2A	chr13:50264918-50266113	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr13:50264404-50266162	NB4	blood:	n/a	chr13:50266048-50266058
9	CEBPB	chr13:50265395-50266198	ECC-1	luminal epithelium:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
10	CEBPB	chr13:50265499-50266180	A549	lung:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
11	TCF7L2	chr13:50265623-50266140	Hela-S3	cervix:	n/a	chr13:50265904-50265918
12	CEBPB	chr13:50265561-50266155	MCF-7	breast:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
13	MAX	chr13:50265069-50266146	ECC-1	luminal epithelium:	n/a	chr13:50266048-50266058
14	E2F6	chr13:50265316-50266125	A549	lung:	n/a	chr13:50265331-50265341
15	MYC	chr13:50264595-50266428	A549	lung:	n/a	chr13:50266048-50266058
16	POLR2A	chr13:50264841-50266121	Hela-S3	cervix:	n/a	n/a
17	MAX	chr13:50265292-50266143	ECC-1	luminal epithelium:	n/a	chr13:50266048-50266058
18	HCFC1	chr13:50264676-50266308	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr13:50265508-50266133	HepG2	liver:	n/a	n/a
20	TCF12	chr13:50265430-50266158	A549	lung:	n/a	n/a
21	POLR2A	chr13:50265228-50266156	MCF10A-Er-Src	breast:	n/a	n/a
22	CEBPB	chr13:50265654-50266110	ECC-1	luminal epithelium:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
23	MAX	chr13:50265278-50266123	HCT-116	colon:	n/a	chr13:50266048-50266058
24	MAZ	chr13:50264334-50266334	IMR90	lung:	n/a	chr13:50266048-50266058
25	MYC	chr13:50265483-50266113	MCF10A-Er-Src	breast:	n/a	chr13:50266048-50266058
26	TEAD4	chr13:50265006-50266126	SK-N-SH	brain:	n/a	n/a
27	MAX	chr13:50265063-50266215	HepG2	liver:	n/a	chr13:50266048-50266058
28	POLR2A	chr13:50265278-50266117	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr13:50264857-50266173	HepG2	liver:	n/a	n/a
30	CEBPB	chr13:50265494-50266305	HCT-116	colon:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
31	POLR2A	chr13:50264417-50266117	HepG2	liver:	n/a	n/a
32	E2F6	chr13:50265307-50266241	H1-hESC	embryonic stem cell:	n/a	chr13:50265331-50265341
33	POLR2A	chr13:50264872-50266268	H1-hESC	embryonic stem cell:	n/a	n/a
34	MXI1	chr13:50264254-50266395	IMR90	lung:	n/a	n/a
35	MTA3	chr13:50265614-50266127	GM12878	blood:	n/a	n/a
36	POLR2A	chr13:50265002-50266151	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr13:50265058-50266132	A549	lung:	n/a	chr13:50266048-50266058
38	POLR2A	chr13:50264315-50266185	SK-N-MC	brain:	n/a	n/a
39	MAX	chr13:50264994-50266158	HCT-116	colon:	n/a	chr13:50266048-50266058
40	POLR2A	chr13:50265280-50266148	ProgFib	skin:	n/a	n/a
41	MXI1	chr13:50264145-50266409	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:50265861..50268328-chr13:50270535..50273310,2	K562	blood:
2	chr13:50266035..50267824-chr13:50362193..50365135,2	K562	blood:
3	chr13:50265388..50266260-chr8:67837758..67838423,2	NB4	blood:
4	chr13:50261767..50269137-chr13:50365068..50368535,12	MCF-7	breast:
5	chr12:53701001..53701522-chr13:50265680..50266200,2	NB4	blood:
6	chr13:50265747..50268429-chr13:50268822..50272035,3	K562	blood:
7	chr13:50262508..50268089-chr13:50363531..50368771,13	MCF-7	breast:
8	chr13:50263387..50266299-chr13:50365424..50368132,3	K562	blood:

Variant related genes	Relation type
EBPL	TF binding region
ENSG00000102753	Chromatin interaction
ENSG00000245910	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12585586	0.97[ASN][1000 genomes]
rs61959939	0.83[AFR][1000 genomes]
rs6561554	0.87[AFR][1000 genomes]
rs6561555	0.87[AFR][1000 genomes]
rs6561557	0.91[ASW][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs7319887	0.85[AFR][1000 genomes]
rs7982132	0.91[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7983905	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7983918	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526596	0.91[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap]
rs9526599	0.88[YRI][hapmap]
rs9535303	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs9535304	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9535308	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9535313	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9535319	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs9535334	0.82[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs9535335	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs9535343	0.82[JPT][hapmap]
rs9562919	0.82[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs9568307	0.85[AFR][1000 genomes]
rs9568313	0.91[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9591292	0.85[AFR][1000 genomes]
rs9596183	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9596187	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]

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	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3809325	EBPL	cis	Adipose Subcutaneous	GTEx
rs3809325	EBPL	cis	Lymphoblastoid	GTEx
rs3809325	EBPL	cis	Artery Aorta	GTEx
rs3809325	EBPL	cis	Esophagus Muscularis	GTEx
rs3809325	EBPL	cis	Artery Tibial	GTEx
rs3809325	EBPL	cis	lymphoblastoid	seeQTL
rs3809325	EBPL	cis	parietal	SCAN
rs3809325	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs3809325	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs3809325	EBPL	cis	Cerebellum	GTEx
rs3809325	EBPL	cis	brain	seeQTL
rs3809325	EBPL	cis	cerebellum	SCAN
rs3809325	EBPL	cis	multi-tissue	Pritchard
rs3809325	EBPL	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50263800-50266200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr13:50264000-50266200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:50264000-50266200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr13:50264000-50266200	Active TSS	HSMM	muscle
5	chr13:50264200-50266200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr13:50264200-50266200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr13:50264200-50266200	Active TSS	Ovary	ovary
8	chr13:50264400-50266200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr13:50264400-50266200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr13:50264400-50266200	Active TSS	Brain Cingulate Gyrus	brain
11	chr13:50264400-50266200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr13:50264400-50266200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:50264400-50266200	Active TSS	Fetal Intestine Small	intestine
14	chr13:50264400-50266200	Active TSS	Fetal Kidney	kidney
15	chr13:50264400-50266200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr13:50264400-50266200	Active TSS	Right Ventricle	heart
17	chr13:50264400-50266200	Active TSS	Thymus	Thymus
18	chr13:50264400-50266200	Active TSS	NHDF-Ad	bronchial
19	chr13:50264400-50266400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:50264400-50266400	Active TSS	Colonic Mucosa	Colon
21	chr13:50264400-50266400	Active TSS	Fetal Brain Female	brain
22	chr13:50264600-50266200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:50264600-50266200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr13:50264600-50266200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr13:50264600-50266200	Active TSS	Brain Hippocampus Middle	brain
26	chr13:50264600-50266200	Active TSS	Left Ventricle	heart
27	chr13:50264600-50266200	Active TSS	Psoas Muscle	Psoas
28	chr13:50264600-50266200	Active TSS	Rectal Smooth Muscle	rectum
29	chr13:50264600-50266400	Active TSS	Esophagus	oesophagus
30	chr13:50264800-50266200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr13:50264800-50266200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:50264800-50266200	Active TSS	Aorta	Aorta
33	chr13:50264800-50266200	Active TSS	Brain Angular Gyrus	brain
34	chr13:50264800-50266200	Active TSS	Fetal Lung	lung
35	chr13:50264800-50266200	Active TSS	Fetal Stomach	stomach
36	chr13:50264800-50266200	Active TSS	Gastric	stomach
37	chr13:50264800-50266200	Active TSS	HSMMtube	muscle
38	chr13:50264800-50266400	Active TSS	Brain Anterior Caudate	brain
39	chr13:50265000-50266200	Active TSS	Brain Substantia Nigra	brain
40	chr13:50265000-50266200	Active TSS	NH-A	brain
41	chr13:50265000-50266400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:50265000-50266400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:50265000-50266400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:50265000-50266400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:50265000-50266400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:50265000-50266400	Active TSS	Liver	Liver
47	chr13:50265000-50266400	Active TSS	Duodenum Mucosa	Duodenum
48	chr13:50265200-50266200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr13:50265200-50266400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr13:50265200-50266400	Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links