Variant report

Variant	rs9568328
Chromosome Location	chr13:50347308-50347309
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50346317..50348509-chr13:50365668..50368332,3	MCF-7	breast:
2	chr13:50344891..50347540-chr13:50347984..50350417,3	MCF-7	breast:
3	chr13:50337999..50340352-chr13:50345226..50347433,2	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1009334	0.95[EUR][1000 genomes]
rs1198314	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198316	1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198318	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1198326	0.95[EUR][1000 genomes]
rs1198331	0.90[EUR][1000 genomes]
rs1923661	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs1967761	0.92[EUR][1000 genomes]
rs2407701	0.90[EUR][1000 genomes]
rs2897769	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3903769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6561564	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs716371	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs7994774	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8000298	0.95[EUR][1000 genomes]
rs8000321	0.95[EUR][1000 genomes]
rs9562920	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562923	1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562924	1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568315	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9568319	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568320	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568327	1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568331	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568332	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957475	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591301	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596178	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9596179	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9596190	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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
rs9568328	EBPL	cis	Thyroid	GTEx
rs9568328	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9568328	EBPL	cis	Artery Tibial	GTEx
rs9568328	EBPL	cis	Skin Sun Exposed Lower leg	GTEx
rs9568328	EBPL	cis	Esophagus Muscularis	GTEx
rs9568328	EBPL	cis	Nerve Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
4	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr13:50324600-50350800	Weak transcription	HSMM	muscle
6	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:50326200-50349000	Weak transcription	Left Ventricle	heart
8	chr13:50328400-50349000	Weak transcription	Lung	lung
9	chr13:50328600-50349000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:50330800-50349000	Weak transcription	HepG2	liver
11	chr13:50334000-50352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr13:50334200-50351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:50334400-50350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:50334400-50351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr13:50334600-50350200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
17	chr13:50335200-50349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
19	chr13:50336400-50351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr13:50336600-50352400	Weak transcription	Thymus	Thymus
21	chr13:50336600-50353800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:50336800-50364600	Weak transcription	NHLF	lung
23	chr13:50338000-50349800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr13:50338000-50353800	Weak transcription	Dnd41	blood
25	chr13:50339200-50353800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:50340600-50351200	Weak transcription	A549	lung
30	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr13:50343400-50351800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:50344000-50355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:50345400-50351200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr13:50345800-50351400	Weak transcription	GM12878-XiMat	blood
35	chr13:50346000-50349000	Weak transcription	Ovary	ovary
36	chr13:50346000-50351600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:50346200-50351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:50347000-50351600	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links