Variant report

Variant	rs942699
Chromosome Location	chr1:76820435-76820436
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76816508..76818358-chr1:76820395..76822942,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11162127	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11162130	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12122625	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12123443	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12123510	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133165	0.81[ASN][1000 genomes]
rs12144344	0.81[ASN][1000 genomes]
rs12239582	0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs12727514	0.90[YRI][hapmap]
rs12737993	0.90[YRI][hapmap]
rs12740580	0.90[YRI][hapmap]
rs12753314	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12755056	0.89[YRI][hapmap]
rs1359468	0.81[ASN][1000 genomes]
rs1359469	0.81[ASN][1000 genomes]
rs1540963	0.83[ASN][1000 genomes]
rs1540964	0.83[ASN][1000 genomes]
rs1570825	0.84[CEU][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17098145	0.90[YRI][hapmap]
rs17098842	0.90[YRI][hapmap]
rs17098859	0.90[YRI][hapmap]
rs1952021	0.81[ASN][1000 genomes]
rs2893413	0.81[ASN][1000 genomes]
rs4288644	0.81[YRI][hapmap]
rs59741131	0.81[ASN][1000 genomes]
rs6593533	0.81[ASN][1000 genomes]
rs6593534	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9437139	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9437145	0.81[ASN][1000 genomes]
rs9437429	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9437435	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006776	chr1:76777323-76899975	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1014231	chr1:76781140-76880630	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs942699	ST6GALNAC5	cis	cerebellum	SCAN
rs942699	CRYZ	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76811400-76822800	Weak transcription	Fetal Stomach	stomach
2	chr1:76817800-76829400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:76817800-76832200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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