Variant report

Variant	rs9526596
Chromosome Location	chr13:50322333-50322334
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:

Extended variants
information (count: 31 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:27)

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	0.91[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]
rs6561557	0.84[ASW][hapmap];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs9526599	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs9535303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[CHB][hapmap];1.00[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	0.84[CHB][hapmap];0.86[JPT][hapmap];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];0.94[CHB][hapmap];0.88[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];1.00[CHB][hapmap];1.00[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]
rs9535343	0.88[JPT][hapmap]
rs9562919	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]
rs9568313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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];1.00[CHB][hapmap];1.00[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9526596	EBPL	cis	Adipose Subcutaneous	GTEx
rs9526596	C20orf175	trans	multi-tissue	Pritchard
rs9526596	EBPL	cis	lymphoblastoid	seeQTL
rs9526596	FAM65C	cis	Liver	GTEx
rs9526596	EBPL	cis	Lymphoblastoid	GTEx
rs9526596	EBPL	cis	parietal	SCAN
rs9526596	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9526596	EBPL	cis	Artery Tibial	GTEx
rs9526596	EBPL	cis	multi-tissue	Pritchard
rs9526596	EBPL	cis	brain	seeQTL
rs9526596	KPNA3	cis	multi-tissue	Pritchard
rs9526596	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9526596	EBPL	cis	lung	GTEx
rs9526596	KPNA3	cis	Liver	GTEx
rs9526596	EBPL	cis	cerebellum	SCAN
rs9526596	LPAR6	cis	cerebellum	SCAN
rs9526596	EBPL	cis	Whole Blood	GTEx
rs9526596	EBPL	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 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	chr13:50297000-50322400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:50301200-50323600	Weak transcription	Colon Smooth Muscle	Colon
17	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
19	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:50306000-50324000	Weak transcription	HSMMtube	muscle
21	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr13:50306200-50323200	Weak transcription	Brain Germinal Matrix	brain
23	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
25	chr13:50306600-50323200	Weak transcription	NHEK	skin
26	chr13:50306800-50333800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
28	chr13:50308200-50324000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:50308200-50324200	Weak transcription	Psoas Muscle	Psoas
30	chr13:50308200-50324200	Weak transcription	NHLF	lung
31	chr13:50308200-50327400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr13:50308200-50327600	Weak transcription	Lung	lung
33	chr13:50314800-50327600	Weak transcription	Gastric	stomach
34	chr13:50315200-50336000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr13:50315400-50324000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr13:50315600-50323000	Weak transcription	Fetal Heart	heart
37	chr13:50317600-50343600	Weak transcription	Primary T cells from cord blood	blood
38	chr13:50318200-50324200	Weak transcription	NHDF-Ad	bronchial
39	chr13:50318400-50324200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:50318800-50333800	Weak transcription	NH-A	brain
41	chr13:50319200-50324000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr13:50319400-50324000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:50319400-50324000	Weak transcription	Osteobl	bone
44	chr13:50319600-50324000	Weak transcription	HSMM	muscle
45	chr13:50319600-50333600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr13:50319600-50334800	Weak transcription	Fetal Lung	lung
47	chr13:50320000-50333600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr13:50320000-50333600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr13:50320000-50333600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr13:50320200-50327600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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