Variant report

Variant	rs56006419
Chromosome Location	chr13:50252579-50252580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50251639..50253630-chr13:50365412..50367568,2	MCF-7	breast:
2	chr13:50251371..50253574-chr13:50364752..50368154,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11839475	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12428286	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1407439	0.82[ASN][1000 genomes]
rs2273817	0.82[ASN][1000 genomes]
rs35150514	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35526541	0.82[ASN][1000 genomes]
rs61959916	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959917	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61959931	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959935	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61959938	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561556	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7321073	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7321709	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332209	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734223	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748678	0.88[ASN][1000 genomes]
rs9535314	0.82[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	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	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56006419	EBPL	cis	Esophagus Mucosa	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50224600-50252600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:50227400-50253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
5	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr13:50237400-50256000	Weak transcription	NH-A	brain
7	chr13:50238800-50253000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:50240600-50253400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
10	chr13:50241800-50253400	Weak transcription	Esophagus	oesophagus
11	chr13:50241800-50256000	Weak transcription	HMEC	breast
12	chr13:50242000-50254000	Weak transcription	Fetal Brain Female	brain
13	chr13:50242200-50253000	Weak transcription	Fetal Thymus	thymus
14	chr13:50242200-50253400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:50242200-50256200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr13:50242200-50264200	Weak transcription	K562	blood
20	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr13:50242400-50254200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:50242400-50256200	Weak transcription	Brain Substantia Nigra	brain
24	chr13:50242400-50260200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr13:50242400-50260400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr13:50242400-50261400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr13:50242400-50261400	Weak transcription	Gastric	stomach
28	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
29	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
32	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
34	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr13:50242600-50260000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr13:50244200-50256200	Weak transcription	Fetal Kidney	kidney
37	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr13:50244600-50253200	Weak transcription	A549	lung
39	chr13:50244600-50255800	Weak transcription	NHDF-Ad	bronchial
40	chr13:50244800-50255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr13:50245200-50253200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr13:50245600-50256000	Weak transcription	Osteobl	bone
43	chr13:50245600-50256200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:50245800-50255800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:50245800-50256400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:50245800-50261400	Weak transcription	HUVEC	blood vessel
47	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
48	chr13:50246200-50261400	Weak transcription	Hela-S3	cervix
49	chr13:50246800-50253200	Strong transcription	HepG2	liver
50	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links