Variant report

Variant	rs13149070
Chromosome Location	chr4:99479684-99479685
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	chr4:96237471..96240020-chr4:99477884..99480366,2	K562	blood:
2	chr4:99479404..99481203-chr4:99500448..99502208,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10002696	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10006366	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10018825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025051	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs11730384	0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13108940	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs13134231	0.94[JPT][hapmap]
rs13141997	0.96[CEU][hapmap]
rs1528547	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1534554	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1534555	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1573478	0.96[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1919211	0.89[JPT][hapmap]
rs2037832	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2866016	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs2866017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699343	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4699345	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs4699348	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4699349	0.92[CEU][hapmap]
rs4699639	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4699640	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4699644	0.96[CEU][hapmap]
rs4699650	0.89[JPT][hapmap]
rs6532742	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs6532748	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs6532751	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs6831643	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs6837359	0.92[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71600251	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7672134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7678323	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13149070	TSPAN5	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466600-99479800	Weak transcription	Fetal Thymus	thymus
2	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:99468400-99482200	Weak transcription	Esophagus	oesophagus
4	chr4:99469000-99482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:99475200-99482400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:99475400-99481400	Enhancers	Brain Hippocampus Middle	brain
7	chr4:99475400-99482000	Enhancers	Brain Cingulate Gyrus	brain
8	chr4:99475400-99482200	Enhancers	Brain Angular Gyrus	brain
9	chr4:99475600-99480600	Enhancers	Brain Germinal Matrix	brain
10	chr4:99475600-99481400	Enhancers	Brain Substantia Nigra	brain
11	chr4:99475800-99482200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr4:99476000-99479800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:99476000-99481200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:99476000-99482200	Enhancers	Fetal Brain Female	brain
15	chr4:99477200-99479800	Enhancers	NHDF-Ad	bronchial
16	chr4:99477200-99482800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:99477400-99480400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:99477400-99486800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:99477400-99487600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:99477400-99487600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:99477800-99482800	Weak transcription	HMEC	breast
22	chr4:99478000-99483000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:99478200-99480200	Enhancers	Fetal Muscle Leg	muscle
24	chr4:99478200-99480200	Enhancers	Ovary	ovary
25	chr4:99478200-99480400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr4:99478200-99481800	Enhancers	Brain Anterior Caudate	brain
27	chr4:99478400-99480200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:99478400-99480200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:99478400-99480200	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:99478400-99480400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:99478600-99481800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:99478600-99482200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:99478800-99480400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:99478800-99480400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr4:99478800-99480400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr4:99478800-99482200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:99479000-99479800	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:99479000-99479800	Weak transcription	Lung	lung
39	chr4:99479000-99480600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr4:99479000-99480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:99479000-99480800	Weak transcription	Fetal Brain Male	brain
42	chr4:99479000-99480800	Weak transcription	Fetal Heart	heart
43	chr4:99479000-99486800	Weak transcription	Fetal Lung	lung
44	chr4:99479000-99490200	Weak transcription	HSMMtube	muscle
45	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
46	chr4:99479200-99480400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr4:99479200-99481200	Weak transcription	HSMM	muscle
48	chr4:99479200-99482200	Weak transcription	NHEK	skin
49	chr4:99479200-99482400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr4:99479200-99482400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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