Variant report

Variant	rs9535309
Chromosome Location	chr13:50295961-50295962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11148160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148161	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12584560	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12585586	0.85[EUR][1000 genomes]
rs12864534	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12875005	0.83[EUR][1000 genomes]
rs12876889	0.86[EUR][1000 genomes]
rs12877931	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1581744	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2025264	0.80[EUR][1000 genomes]
rs34423763	0.86[EUR][1000 genomes]
rs35331571	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7446	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7987502	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7997798	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526592	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526600	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9535301	0.86[ASN][1000 genomes]
rs9535302	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535315	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535332	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535337	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9568309	0.86[ASN][1000 genomes]
rs9646001	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535309	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9535309	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50296000	Weak transcription	K562	blood
2	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:50266200-50307800	Weak transcription	Gastric	stomach
5	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
7	chr13:50272400-50296000	Weak transcription	Fetal Heart	heart
8	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
9	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:50276000-50299800	Weak transcription	Right Ventricle	heart
11	chr13:50276000-50307600	Weak transcription	Pancreas	Pancrea
12	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
13	chr13:50280000-50308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:50280600-50296000	Weak transcription	Colon Smooth Muscle	Colon
15	chr13:50283000-50296000	Weak transcription	HSMMtube	muscle
16	chr13:50289600-50296800	Strong transcription	Fetal Thymus	thymus
17	chr13:50289800-50296000	Weak transcription	GM12878-XiMat	blood
18	chr13:50289800-50296600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:50290000-50296000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr13:50290000-50296000	Weak transcription	HepG2	liver
21	chr13:50290000-50296600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr13:50290000-50297000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:50290000-50297000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:50290000-50297000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr13:50290000-50298800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr13:50290000-50299400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:50290000-50304600	Strong transcription	Liver	Liver
28	chr13:50290000-50306200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:50290000-50306800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr13:50290200-50297000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr13:50290200-50297200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:50290200-50304600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:50290200-50316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:50290400-50297000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr13:50290400-50297000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr13:50290400-50306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:50290400-50307200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr13:50290600-50296600	Strong transcription	Primary T cells from cord blood	blood
41	chr13:50290600-50297000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr13:50290600-50304400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:50290800-50296600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr13:50290800-50297000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:50290800-50297000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr13:50290800-50297400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:50290800-50301400	Strong transcription	Placenta	Placenta
48	chr13:50290800-50302600	Strong transcription	Adipose Nuclei	Adipose
49	chr13:50290800-50304200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:50291000-50297000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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