Variant report

Variant	rs9535289
Chromosome Location	chr13:50240625-50240626
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:50240541-50240735	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50240420..50241989-chr13:50245723..50247987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203547	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1061979	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139051	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969738	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146142	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34480126	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67155750	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67394151	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67881093	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71216551	0.93[EUR][1000 genomes]
rs7326633	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329488	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991234	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526586	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535284	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535285	0.90[EUR][1000 genomes]
rs9535286	0.90[EUR][1000 genomes]
rs9535293	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9535294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535295	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535298	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535301	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535289	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9535289	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50210600-50241000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:50217800-50241000	Weak transcription	K562	blood
3	chr13:50220000-50245400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:50224600-50243000	Weak transcription	Brain Germinal Matrix	brain
5	chr13:50224600-50252600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:50226400-50244000	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:50226800-50241200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:50227000-50241200	Weak transcription	GM12878-XiMat	blood
9	chr13:50227400-50253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:50227800-50241000	Weak transcription	Fetal Brain Male	brain
11	chr13:50228400-50241200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr13:50228600-50242000	Weak transcription	HSMMtube	muscle
13	chr13:50228600-50244000	Weak transcription	Fetal Kidney	kidney
14	chr13:50229800-50243400	Weak transcription	Small Intestine	intestine
15	chr13:50230000-50241000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:50230200-50241200	Weak transcription	HMEC	breast
17	chr13:50230200-50242000	Weak transcription	NHDF-Ad	bronchial
18	chr13:50230400-50243400	Strong transcription	Fetal Stomach	stomach
19	chr13:50230600-50241200	Weak transcription	Fetal Brain Female	brain
20	chr13:50231000-50241000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:50231000-50246800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr13:50231200-50241000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr13:50231200-50241800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:50231400-50241800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:50231400-50243000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr13:50231800-50241800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr13:50232200-50242400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:50232800-50241800	Weak transcription	Brain Substantia Nigra	brain
30	chr13:50233000-50242600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:50233200-50241200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr13:50233400-50241400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr13:50233400-50242000	Strong transcription	Liver	Liver
34	chr13:50233600-50242400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:50233600-50242600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr13:50233800-50242400	Strong transcription	Dnd41	blood
37	chr13:50234200-50244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr13:50234400-50243600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:50234400-50245400	Weak transcription	Psoas Muscle	Psoas
40	chr13:50234600-50242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:50235400-50252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
43	chr13:50236000-50244000	Weak transcription	Brain Anterior Caudate	brain
44	chr13:50236200-50241200	Weak transcription	Primary B cells from cord blood	blood
45	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr13:50237200-50241600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:50237400-50241200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr13:50237400-50241400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:50237400-50256000	Weak transcription	NH-A	brain
50	chr13:50237600-50241200	Weak transcription	Primary B cells from peripheral blood	blood

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