Variant report

Variant	rs9535328
Chromosome Location	chr13:50334693-50334694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12585586	0.80[ASN][1000 genomes]
rs2146437	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2897771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561563	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982132	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526599	0.80[AFR][1000 genomes]
rs9535304	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535308	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535334	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535335	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568313	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568330	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596183	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs9535328	EBPL	cis	lung	GTEx
rs9535328	EBPL	cis	Adipose Subcutaneous	GTEx
rs9535328	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9535328	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9535328	EBPL	cis	Esophagus Muscularis	GTEx
rs9535328	EBPL	cis	Artery Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50296600-50338600	Weak transcription	Ovary	ovary
3	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
6	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
7	chr13:50315200-50336000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:50317600-50343600	Weak transcription	Primary T cells from cord blood	blood
9	chr13:50319600-50334800	Weak transcription	Fetal Lung	lung
10	chr13:50320400-50336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:50320600-50334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr13:50320600-50334800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr13:50320600-50337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:50320600-50337800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr13:50320800-50340400	Weak transcription	HUVEC	blood vessel
16	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr13:50324400-50340400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr13:50324600-50350800	Weak transcription	HSMM	muscle
19	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:50324800-50338600	Weak transcription	Right Atrium	heart
21	chr13:50326200-50349000	Weak transcription	Left Ventricle	heart
22	chr13:50328200-50338600	Weak transcription	Right Ventricle	heart
23	chr13:50328400-50338600	Weak transcription	Pancreas	Pancrea
24	chr13:50328400-50349000	Weak transcription	Lung	lung
25	chr13:50328600-50349000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:50330600-50334800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:50330800-50349000	Weak transcription	HepG2	liver
28	chr13:50333000-50335200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr13:50333200-50335200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr13:50333400-50334800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr13:50333400-50335200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:50333400-50335200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr13:50333400-50335200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr13:50333400-50335400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:50333400-50338800	Weak transcription	Fetal Heart	heart
36	chr13:50333600-50335000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
37	chr13:50333600-50335000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr13:50333600-50335200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr13:50333600-50335200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:50333600-50335400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr13:50333600-50335400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:50333600-50335600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr13:50333600-50336200	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr13:50333800-50334800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr13:50333800-50335000	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr13:50333800-50335200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr13:50333800-50335200	ZNF genes & repeats	Fetal Thymus	thymus
48	chr13:50333800-50335200	ZNF genes & repeats	Thymus	Thymus
49	chr13:50333800-50335200	Enhancers	GM12878-XiMat	blood
50	chr13:50333800-50335400	ZNF genes & repeats	Fetal Intestine Large	intestine

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