Variant report

Variant	rs9562919
Chromosome Location	chr13:50323808-50323809
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50312252..50315193-chr13:50321361..50323993,2	MCF-7	breast:
2	chr13:50318990..50321781-chr13:50323310..50326144,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12585586	0.80[ASN][1000 genomes]
rs2146437	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2897771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809325	0.82[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs6561557	0.84[YRI][hapmap]
rs6561563	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982132	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526596	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526599	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs9535303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs9535304	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535308	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535313	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535319	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568313	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568330	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596183	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596187	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9562919	EBPL	cis	Whole Blood	GTEx
rs9562919	EBPL	cis	Artery Tibial	GTEx
rs9562919	EBPL	cis	multi-tissue	Pritchard
rs9562919	EBPL	cis	Esophagus Muscularis	GTEx
rs9562919	EBPL	cis	Adipose Subcutaneous	GTEx
rs9562919	EBPL	cis	Lymphoblastoid	GTEx
rs9562919	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9562919	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9562919	EBPL	cis	lung	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
3	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
7	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
11	chr13:50296600-50338600	Weak transcription	Ovary	ovary
12	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
17	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:50306000-50324000	Weak transcription	HSMMtube	muscle
19	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
22	chr13:50306800-50333800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
24	chr13:50308200-50324000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr13:50308200-50324200	Weak transcription	Psoas Muscle	Psoas
26	chr13:50308200-50324200	Weak transcription	NHLF	lung
27	chr13:50308200-50327400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr13:50308200-50327600	Weak transcription	Lung	lung
29	chr13:50314800-50327600	Weak transcription	Gastric	stomach
30	chr13:50315200-50336000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr13:50315400-50324000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr13:50317600-50343600	Weak transcription	Primary T cells from cord blood	blood
33	chr13:50318200-50324200	Weak transcription	NHDF-Ad	bronchial
34	chr13:50318400-50324200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:50318800-50333800	Weak transcription	NH-A	brain
36	chr13:50319200-50324000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr13:50319400-50324000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:50319400-50324000	Weak transcription	Osteobl	bone
39	chr13:50319600-50324000	Weak transcription	HSMM	muscle
40	chr13:50319600-50333600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr13:50319600-50334800	Weak transcription	Fetal Lung	lung
42	chr13:50320000-50333600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr13:50320000-50333600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr13:50320000-50333600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr13:50320200-50327600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr13:50320400-50325800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr13:50320400-50336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr13:50320600-50324200	Weak transcription	Placenta	Placenta
49	chr13:50320600-50324400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:50320600-50324400	Weak transcription	Left Ventricle	heart

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