Variant report

Variant	rs1699007
Chromosome Location	chr6:38583368-38583369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10807196	0.84[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs10807198	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947752	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1321056	1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699002	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1699003	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699004	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1699005	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1699017	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1739621	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739626	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1739627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1739628	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1739629	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1739630	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1739632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1739633	0.82[ASW][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[ASN][1000 genomes]
rs1781708	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1781711	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1781712	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1781738	0.82[EUR][1000 genomes]
rs1852979	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2144328	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252550	0.96[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2736655	1.00[LWK][hapmap]
rs2748172	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2814883	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2814885	0.81[EUR][1000 genomes]
rs2814889	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2814894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4236060	0.82[ASW][hapmap]
rs4392718	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs6458059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394521	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1699007	GLO1	cis	parietal	SCAN
rs1699007	GLO1	cis	cerebellum	SCAN
rs1699007	DNAH8	cis	cerebellum	SCAN
rs1699007	BYSL	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38565400-38589200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:38565800-38583600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:38568200-38584200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:38572000-38591600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:38580600-38600200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:38580600-38601800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:38580800-38585800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:38580800-38589400	Weak transcription	Right Atrium	heart
9	chr6:38580800-38594000	Weak transcription	Small Intestine	intestine
10	chr6:38580800-38604400	Weak transcription	Ovary	ovary
11	chr6:38581000-38585800	Weak transcription	HSMMtube	muscle
12	chr6:38581000-38586200	Weak transcription	Osteobl	bone
13	chr6:38581200-38585800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:38581400-38585800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:38581800-38585800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:38582200-38587200	Weak transcription	Psoas Muscle	Psoas
17	chr6:38582600-38587200	Weak transcription	Right Ventricle	heart
18	chr6:38583000-38599200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:38583200-38583400	Enhancers	Left Ventricle	heart
20	chr6:38583200-38583800	Strong transcription	Primary T cells from cord blood	blood

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