Variant report

Variant	rs1407440
Chromosome Location	chr13:50286218-50286219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50279309..50282316-chr13:50283856..50287335,3	K562	blood:
2	chr13:50284596..50287038-chr13:50289146..50291818,2	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 32 )
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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1211304	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1547623	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1581745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2025263	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2146143	0.92[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];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2407804	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2897770	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3851162	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4942863	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6561552	0.81[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs6561560	0.92[CEU][hapmap];1.00[GIH][hapmap]
rs7330392	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7983303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7984061	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[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];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9526591	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526593	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526594	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9535305	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535307	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535310	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]
rs9535316	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535340	0.80[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:4 , 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	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
3	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
4	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
rs1407440	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs1407440	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs1407440	KCNRG	cis	cerebellum	SCAN
rs1407440	EBPL	cis	cerebellum	SCAN
rs1407440	HTR2A	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50289400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr13:50266200-50289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr13:50266200-50295200	Weak transcription	Spleen	Spleen
4	chr13:50266200-50296000	Weak transcription	K562	blood
5	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:50266200-50307800	Weak transcription	Gastric	stomach
8	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:50266400-50289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr13:50266400-50293600	Weak transcription	Colonic Mucosa	Colon
11	chr13:50266400-50295800	Weak transcription	Small Intestine	intestine
12	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
13	chr13:50267200-50289400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:50270400-50286400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:50271400-50286400	Strong transcription	Dnd41	blood
16	chr13:50271400-50286800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:50272400-50295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:50272400-50296000	Weak transcription	Fetal Heart	heart
19	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
20	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:50274000-50286600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr13:50274200-50286400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr13:50274200-50286400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:50275400-50286400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:50275800-50289200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:50275800-50290000	Weak transcription	Brain Substantia Nigra	brain
27	chr13:50276000-50286400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:50276000-50288400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr13:50276000-50289600	Weak transcription	Fetal Brain Male	brain
30	chr13:50276000-50289600	Weak transcription	Fetal Brain Female	brain
31	chr13:50276000-50291800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:50276000-50299800	Weak transcription	Right Ventricle	heart
33	chr13:50276000-50307600	Weak transcription	Pancreas	Pancrea
34	chr13:50276200-50288600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
36	chr13:50278000-50286400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr13:50278800-50286400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr13:50278800-50286400	Strong transcription	Primary B cells from cord blood	blood
39	chr13:50278800-50286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:50279000-50286400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr13:50279200-50286800	Strong transcription	Fetal Thymus	thymus
42	chr13:50279400-50286400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr13:50279800-50289200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:50280000-50308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:50280200-50295200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr13:50280400-50288600	Weak transcription	Brain Anterior Caudate	brain
47	chr13:50280400-50289400	Weak transcription	Fetal Kidney	kidney
48	chr13:50280400-50289600	Weak transcription	Brain Angular Gyrus	brain
49	chr13:50280400-50290200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr13:50280400-50291600	Weak transcription	HMEC	breast

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