Variant report

Variant	rs8003569
Chromosome Location	chr14:63695667-63695668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10135991	0.83[EUR][1000 genomes]
rs10138015	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10145453	0.83[EUR][1000 genomes]
rs10150464	0.85[EUR][1000 genomes]
rs10483766	0.85[EUR][1000 genomes]
rs1467422	0.89[MEX][hapmap]
rs17100922	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17100931	0.85[EUR][1000 genomes]
rs17100932	0.84[EUR][1000 genomes]
rs17224610	0.85[EUR][1000 genomes]
rs17824443	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1884093	0.91[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs2057133	0.81[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2057134	0.85[EUR][1000 genomes]
rs4902215	0.89[MEX][hapmap]
rs6573499	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6573500	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7144902	0.85[EUR][1000 genomes]
rs7145040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7151486	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154910	0.91[EUR][1000 genomes]
rs7157513	0.95[EUR][1000 genomes]
rs8007945	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8012836	0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs8013068	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527251	chr14:63400786-64068806	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv520528	chr14:63400786-64157117	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv564893	chr14:63526931-63796122	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1045599	chr14:63540073-63765152	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv530774	chr14:63591348-64029881	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8003569	SIX1	cis	cerebellum	SCAN
rs8003569	FLJ43390	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:63672000-63717000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:63676200-63707600	Weak transcription	Aorta	Aorta
3	chr14:63676400-63733600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr14:63679400-63717000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr14:63688600-63696000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr14:63691200-63716800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:63691400-63712800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr14:63691600-63698800	Weak transcription	Fetal Heart	heart
9	chr14:63691600-63705800	Weak transcription	Fetal Stomach	stomach
10	chr14:63691600-63712400	Weak transcription	Ovary	ovary
11	chr14:63694400-63697400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr14:63694800-63696000	Weak transcription	Fetal Lung	lung
13	chr14:63694800-63696000	Weak transcription	NH-A	brain
14	chr14:63694800-63699600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr14:63695000-63696200	Weak transcription	Fetal Muscle Leg	muscle
16	chr14:63695000-63697000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr14:63695600-63695800	Flanking Active TSS	HUVEC	blood vessel
18	chr14:63695600-63696000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr14:63695600-63696200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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