Variant report

Variant	rs315976
Chromosome Location	chr8:87742065-87742066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10094222	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1009574	0.87[JPT][hapmap]
rs1031649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[ASN][1000 genomes]
rs10956948	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1219096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13252425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs13278423	0.95[JPT][hapmap]
rs1372170	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1379739	0.90[CEU][hapmap];0.96[GIH][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1379742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1441238	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[YRI][hapmap]
rs1458119	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1458134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1545221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs1596027	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap]
rs16916907	0.91[JPT][hapmap]
rs2013536	0.87[JPT][hapmap]
rs2885471	0.86[JPT][hapmap]
rs2919754	0.95[ASN][1000 genomes]
rs2957792	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.95[ASN][1000 genomes]
rs315963	0.95[ASN][1000 genomes]
rs315964	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs315965	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs315972	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315973	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs315977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735967	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap]
rs4960985	0.86[JPT][hapmap]
rs4961211	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7002468	0.86[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7002965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7003307	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes]
rs7012836	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7014125	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[YRI][hapmap];0.95[ASN][1000 genomes]
rs7357579	0.81[CEU][hapmap]
rs7814749	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs7842410	0.83[JPT][hapmap]
rs971146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs978134	0.95[JPT][hapmap]
rs996077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]

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	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv891151	chr8:87690019-87776019	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1026794	chr8:87698639-87957840	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv539662	chr8:87698639-87957840	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs315976	CNGB3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87736800-87752400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:87739200-87743200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:87741800-87742400	Enhancers	Fetal Brain Female	brain
4	chr8:87741800-87742600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:87742000-87742400	Enhancers	Brain Cingulate Gyrus	brain
6	chr8:87742000-87742600	Enhancers	Brain Hippocampus Middle	brain

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