Variant report

Variant	rs1325286
Chromosome Location	chr1:76824487-76824488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11162121	0.81[JPT][hapmap]
rs11162131	0.87[AFR][1000 genomes]
rs11162132	0.93[ASW][hapmap];0.83[LWK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs11162133	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs12060625	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12071740	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12075208	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12076310	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12084205	0.82[YRI][hapmap]
rs12089135	0.83[EUR][1000 genomes]
rs12144641	0.93[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs17627490	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17627816	0.90[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17672913	0.82[CHB][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap]
rs28647864	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4342892	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs4638174	0.96[YRI][hapmap]
rs4949629	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949706	0.81[JPT][hapmap]
rs4949710	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4949715	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs58918633	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6659588	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6688662	0.87[ASW][hapmap];0.84[YRI][hapmap]
rs73004234	0.87[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1325286	CRYZ	cis	parietal	SCAN
rs1325286	LHX8	cis	parietal	SCAN
rs1325286	ST6GALNAC3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

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

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