Variant report

Variant	rs9535305
Chromosome Location	chr13:50290415-50290416
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50284596..50287038-chr13:50289146..50291818,2	K562	blood:
2	chr13:50289905..50291806-chr13:50365291..50367807,2	MCF-7	breast:
3	chr13:50264322..50267072-chr13:50288561..50291011,2	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction
ENSG00000123179	Chromatin interaction

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

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

rs_ID	r²[population]
rs1127021	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1407440	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1407441	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1547623	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1581745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2025263	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2146143	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs2181185	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2407804	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2897770	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851162	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4942863	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6561552	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs6561560	0.92[CEU][hapmap]
rs7330392	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7983303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7984061	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9316474	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526591	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9526593	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526594	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9535307	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535310	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535316	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535340	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9535341	0.95[YRI][hapmap]
rs9562927	0.95[YRI][hapmap]

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
rs9535305	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9535305	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50295200	Weak transcription	Spleen	Spleen
2	chr13:50266200-50296000	Weak transcription	K562	blood
3	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr13:50266200-50307800	Weak transcription	Gastric	stomach
6	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:50266400-50293600	Weak transcription	Colonic Mucosa	Colon
8	chr13:50266400-50295800	Weak transcription	Small Intestine	intestine
9	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
10	chr13:50272400-50295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:50272400-50296000	Weak transcription	Fetal Heart	heart
12	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
13	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:50276000-50291800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:50276000-50299800	Weak transcription	Right Ventricle	heart
16	chr13:50276000-50307600	Weak transcription	Pancreas	Pancrea
17	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
18	chr13:50280000-50308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:50280200-50295200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr13:50280400-50291600	Weak transcription	HMEC	breast
21	chr13:50280600-50295800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr13:50280600-50296000	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:50283000-50296000	Weak transcription	HSMMtube	muscle
24	chr13:50283400-50294600	Weak transcription	Lung	lung
25	chr13:50284000-50293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:50284600-50292000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr13:50284800-50290800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr13:50285000-50290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:50285000-50291000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr13:50285200-50295200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr13:50286400-50290600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr13:50286400-50290800	Weak transcription	Placenta	Placenta
33	chr13:50287800-50291400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr13:50287800-50293000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:50288000-50291200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:50288200-50290600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:50288200-50291000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr13:50288400-50291000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
39	chr13:50288400-50291200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr13:50289000-50290600	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr13:50289200-50291200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:50289200-50291200	ZNF genes & repeats	Dnd41	blood
43	chr13:50289400-50291000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr13:50289400-50292200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr13:50289600-50290800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr13:50289600-50290800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:50289600-50290800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:50289600-50290800	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr13:50289600-50291000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr13:50289600-50291000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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