Variant report

Variant	rs9568330
Chromosome Location	chr13:50353353-50353354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50352653..50354938-chr13:50357340..50359158,2	MCF-7	breast:
2	chr13:50351267..50358317-chr13:50361760..50368621,11	MCF-7	breast:
3	chr13:50244133..50245695-chr13:50352710..50354837,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EBPL-2	chr13:50351804-50354609	ENSG00000224798.1

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2146437	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897771	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782930	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6561563	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338721	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7982132	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9526596	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526599	0.87[AFR][1000 genomes]
rs9535304	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535308	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535313	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535319	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535321	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535328	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535334	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535335	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562919	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568313	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9568317	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596183	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596186	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596187	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	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
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1038	chr13:50324773-50359990	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9568330	EBPL	cis	lung	GTEx
rs9568330	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9568330	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9568330	EBPL	cis	Artery Tibial	GTEx
rs9568330	EBPL	cis	Esophagus Muscularis	GTEx
rs9568330	EBPL	cis	Whole Blood	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
2	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
4	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
5	chr13:50336600-50353800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:50336800-50364600	Weak transcription	NHLF	lung
7	chr13:50338000-50353800	Weak transcription	Dnd41	blood
8	chr13:50339200-50353800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr13:50344000-50355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:50349600-50353600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:50349600-50357600	Weak transcription	Gastric	stomach
16	chr13:50349600-50357600	Weak transcription	Left Ventricle	heart
17	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:50349600-50365400	Weak transcription	Lung	lung
19	chr13:50349800-50355200	Weak transcription	Fetal Heart	heart
20	chr13:50350000-50353800	Weak transcription	Brain Substantia Nigra	brain
21	chr13:50350400-50356200	Weak transcription	Ovary	ovary
22	chr13:50350600-50358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:50351200-50364200	Weak transcription	HSMM	muscle
24	chr13:50351200-50364600	Weak transcription	HSMMtube	muscle
25	chr13:50351400-50353800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr13:50351400-50354000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:50351400-50354400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr13:50351400-50362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:50351400-50363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr13:50351600-50353800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr13:50351600-50354000	Weak transcription	Right Ventricle	heart
32	chr13:50351600-50355600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:50351600-50359200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:50351600-50359200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr13:50351600-50360800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:50351600-50363800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:50351800-50354400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:50351800-50354400	Enhancers	HepG2	liver
39	chr13:50351800-50354600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr13:50351800-50359400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:50351800-50363800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:50351800-50364000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr13:50352000-50353800	Weak transcription	Psoas Muscle	Psoas
44	chr13:50352000-50356000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr13:50352000-50365200	Weak transcription	Fetal Thymus	thymus
46	chr13:50352400-50364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr13:50352600-50353400	Weak transcription	Brain Angular Gyrus	brain
48	chr13:50352600-50353600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr13:50352600-50353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:50352600-50353800	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links