Variant report

Variant	rs1885758
Chromosome Location	chr13:40145536-40145537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1022808	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1022810	0.82[CEU][hapmap]
rs1160321	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1570414	0.93[CEU][hapmap]
rs17236046	0.81[AMR][1000 genomes]
rs1885760	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1885762	0.87[EUR][1000 genomes]
rs1885763	0.82[CEU][hapmap]
rs2324335	0.81[ASN][1000 genomes]
rs2324347	1.00[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes]
rs2875329	1.00[CEU][hapmap]
rs3812881	0.81[CEU][hapmap]
rs3858867	0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4325425	1.00[CEU][hapmap]
rs4456374	0.95[AMR][1000 genomes]
rs4520717	1.00[CEU][hapmap]
rs4941933	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4941935	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4943674	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5010893	0.81[AMR][1000 genomes]
rs61956469	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6563719	0.82[CEU][hapmap]
rs6563720	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6563726	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6563727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563728	0.89[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7319551	0.86[GIH][hapmap]
rs7324883	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];1.00[ASN][1000 genomes]
rs7333587	0.93[CEU][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs7338428	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7981205	0.86[AMR][1000 genomes]
rs7985507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927515	0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes]
rs9285136	1.00[CEU][hapmap]
rs9315704	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315705	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs9548796	1.00[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9548807	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9566448	0.87[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs9566457	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs9576865	1.00[CEU][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs978135	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1885758	ALG5	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40132200-40145600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:40135800-40145600	Weak transcription	Lung	lung
5	chr13:40136400-40145600	Weak transcription	Right Ventricle	heart
6	chr13:40138800-40152800	Weak transcription	Aorta	Aorta
7	chr13:40139200-40158000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:40139800-40146400	Weak transcription	Brain Substantia Nigra	brain
9	chr13:40140000-40145600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:40140000-40169400	Weak transcription	Fetal Stomach	stomach
11	chr13:40140200-40145600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr13:40140200-40149600	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:40140400-40157800	Weak transcription	Adipose Nuclei	Adipose
14	chr13:40140600-40146600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:40140600-40148600	Weak transcription	Fetal Lung	lung
16	chr13:40140800-40152800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr13:40140800-40165400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:40141200-40145600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:40141200-40145600	Weak transcription	NHLF	lung
20	chr13:40142000-40148800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:40142000-40156200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:40142000-40156200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr13:40142000-40169400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:40142000-40169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:40142200-40150000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:40142200-40152600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr13:40143000-40149400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr13:40143000-40158200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr13:40143200-40157800	Weak transcription	NHDF-Ad	bronchial
30	chr13:40143200-40161800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr13:40143200-40170800	Weak transcription	Osteobl	bone
32	chr13:40143400-40145600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:40143400-40145800	Weak transcription	Ovary	ovary
34	chr13:40143600-40145600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:40144400-40147200	Enhancers	Fetal Heart	heart
36	chr13:40144800-40146400	Enhancers	Left Ventricle	heart
37	chr13:40145200-40145800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:40145400-40146200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:40145400-40146400	Enhancers	Right Atrium	heart

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