Variant report

Variant	rs9535310
Chromosome Location	chr13:50296026-50296027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1127021	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1211304	1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1407440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1407441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1547623	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1581745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2025263	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2146143	0.93[CEU][hapmap];0.87[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs2181185	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2407804	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2897770	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3851162	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4942863	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6561552	0.81[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs6561560	0.92[CEU][hapmap];1.00[GIH][hapmap]
rs7330392	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7983303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7984061	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9316474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9526591	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526594	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9535305	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535307	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535316	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535340	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535341	0.88[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs9562927	0.88[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535310	EBPL	cis	cerebellum	SCAN
rs9535310	HTR2A	cis	parietal	SCAN
rs9535310	KCNRG	cis	cerebellum	SCAN
rs9535310	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9535310	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:50266200-50307800	Weak transcription	Gastric	stomach
4	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
6	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
7	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:50276000-50299800	Weak transcription	Right Ventricle	heart
9	chr13:50276000-50307600	Weak transcription	Pancreas	Pancrea
10	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
11	chr13:50280000-50308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:50289600-50296800	Strong transcription	Fetal Thymus	thymus
13	chr13:50289800-50296600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:50290000-50296600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr13:50290000-50297000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:50290000-50297000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:50290000-50297000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr13:50290000-50298800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr13:50290000-50299400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr13:50290000-50304600	Strong transcription	Liver	Liver
21	chr13:50290000-50306200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:50290000-50306800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr13:50290200-50297000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:50290200-50297200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:50290200-50304600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:50290200-50316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr13:50290400-50297000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:50290400-50297000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr13:50290400-50306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:50290400-50307200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:50290600-50296600	Strong transcription	Primary T cells from cord blood	blood
34	chr13:50290600-50297000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr13:50290600-50304400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:50290800-50296600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr13:50290800-50297000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:50290800-50297000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr13:50290800-50297400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:50290800-50301400	Strong transcription	Placenta	Placenta
41	chr13:50290800-50302600	Strong transcription	Adipose Nuclei	Adipose
42	chr13:50290800-50304200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:50291000-50297000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr13:50291000-50297000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr13:50291000-50297000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:50291000-50301200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr13:50291000-50301200	Strong transcription	HSMM	muscle
48	chr13:50291000-50306800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:50291000-50306800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr13:50291200-50296800	Strong transcription	Primary hematopoietic stem cells	blood

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