Variant report

Variant	rs6469298
Chromosome Location	chr8:89222426-89222427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10091022	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10099839	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10104620	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110977	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113080	0.96[EUR][1000 genomes]
rs13256568	0.96[EUR][1000 genomes]
rs13261169	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13264048	0.95[EUR][1000 genomes]
rs13439559	0.96[EUR][1000 genomes]
rs16879913	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16881281	0.86[CEU][hapmap]
rs28542805	0.81[ASN][1000 genomes]
rs28589951	0.81[ASN][1000 genomes]
rs28639477	0.81[ASN][1000 genomes]
rs28649468	0.96[EUR][1000 genomes]
rs28678551	0.96[EUR][1000 genomes]
rs28730305	0.81[ASN][1000 genomes]
rs28904614	0.96[EUR][1000 genomes]
rs28904635	1.00[ASN][1000 genomes]
rs7357573	0.96[EUR][1000 genomes]
rs7357575	0.96[EUR][1000 genomes]
rs7357576	0.96[EUR][1000 genomes]
rs7821734	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1029898	chr8:88837956-89606641	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1030028	chr8:89060085-89733470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1019111	chr8:89186908-89475460	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831386	chr8:89209788-89403546	Enhancers Genic enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv527243	chr8:89217541-89227970	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3346665	chr8:89221136-89222934	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6469298	IGSF3	trans	lymphoblastoid	seeQTL
rs6469298	CNGB3	cis	cerebellum	SCAN
rs6469298	LOC338579	trans	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89215200-89227600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr8:89217800-89231400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:89218200-89223800	Weak transcription	NH-A	brain
4	chr8:89218800-89224200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:89220000-89223600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:89220000-89227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr8:89220200-89222600	Weak transcription	Fetal Intestine Large	intestine
8	chr8:89220200-89227800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:89220600-89227600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:89220600-89227800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:89222000-89222800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:89222400-89223600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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