Variant report

Variant	rs9535334
Chromosome Location	chr13:50343886-50343887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50341914..50345119-chr13:50364352..50368187,3	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2146437	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2897771	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782930	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7338721	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7982132	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9526596	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]
rs9526599	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9535303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs9535304	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535308	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535313	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535319	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535321	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535328	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562919	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]
rs9568313	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568317	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568330	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596183	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9596186	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596187	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9535334	EBPL	cis	Esophagus Muscularis	GTEx
rs9535334	EBPL	cis	Adipose Subcutaneous	GTEx
rs9535334	EBPL	cis	Lymphoblastoid	GTEx
rs9535334	EBPL	cis	multi-tissue	Pritchard
rs9535334	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9535334	EBPL	cis	Whole Blood	GTEx
rs9535334	EBPL	cis	lung	GTEx
rs9535334	EBPL	cis	Artery Tibial	GTEx
rs9535334	KPNA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
5	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr13:50324600-50350800	Weak transcription	HSMM	muscle
7	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:50326200-50349000	Weak transcription	Left Ventricle	heart
9	chr13:50328400-50349000	Weak transcription	Lung	lung
10	chr13:50328600-50349000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr13:50330800-50349000	Weak transcription	HepG2	liver
12	chr13:50334000-50352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr13:50334200-50351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:50334400-50350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:50334400-50351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr13:50334600-50350200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
18	chr13:50335200-50347200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr13:50335200-50349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
21	chr13:50336400-50351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:50336600-50352400	Weak transcription	Thymus	Thymus
23	chr13:50336600-50353800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:50336800-50364600	Weak transcription	NHLF	lung
25	chr13:50338000-50349800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr13:50338000-50353800	Weak transcription	Dnd41	blood
27	chr13:50338200-50345400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr13:50338200-50346000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:50338800-50345600	Weak transcription	Ovary	ovary
30	chr13:50338800-50345800	Weak transcription	Psoas Muscle	Psoas
31	chr13:50339200-50353800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:50340600-50351200	Weak transcription	A549	lung
36	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr13:50343400-50351800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:50343600-50344000	Strong transcription	Primary T cells from cord blood	blood
39	chr13:50343600-50344000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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