Variant report

Variant	rs1824347
Chromosome Location	chr4:173764577-173764578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1026505	0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1116651	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap]
rs1116652	1.00[JPT][hapmap]
rs11935653	1.00[JPT][hapmap]
rs12512152	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13112941	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1350586	1.00[JPT][hapmap]
rs1459155	0.84[ASN][1000 genomes]
rs1459156	0.90[ASN][1000 genomes]
rs17058964	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17058973	1.00[JPT][hapmap]
rs17058981	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17318218	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17318489	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1903126	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1947639	0.92[ASN][1000 genomes]
rs28718496	0.90[ASN][1000 genomes]
rs34547986	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35447014	0.92[ASN][1000 genomes]
rs6553659	0.92[ASN][1000 genomes]
rs6833917	0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6844018	0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7660673	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7673435	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7691157	1.00[JPT][hapmap]
rs898197	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9637709	0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9637710	0.90[ASN][1000 genomes]
rs9968432	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3327952	chr4:173591786-173805861	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv968039	chr4:173753530-173772714	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv881394	chr4:173757115-173847405	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1824347	GALNTL6	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173747600-173765600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:173762200-173771800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:173763600-173764600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:173763600-173765000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:173763800-173764800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:173764000-173764800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:173764000-173764800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:173764400-173764600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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