Variant report

Variant	rs11265079
Chromosome Location	chr1:158793852-158793853
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11265075	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265077	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265078	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265081	0.87[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11265085	0.87[CEU][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap]
rs11805139	0.87[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12081375	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12089272	0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12090080	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12092047	0.93[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092347	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096549	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12096611	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13375797	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2106090	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2106091	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2325697	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28532901	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2875712	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56257984	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56371861	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58009120	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59462228	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72702926	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72702928	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7513873	0.91[ASW][hapmap];0.87[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7545956	0.87[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006288	chr1:158684002-158844221	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv535181	chr1:158684002-158844221	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv817245	chr1:158684003-158844220	Enhancers Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv547988	chr1:158685036-158848064	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv547989	chr1:158685036-158852953	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1011085	chr1:158703583-158845135	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1002401	chr1:158712627-158972031	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv870369	chr1:158758091-158796383	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11265079	EFNA4	cis	parietal	SCAN
rs11265079	SLAMF6	cis	cerebellum	SCAN
rs11265079	RUSC1	cis	parietal	SCAN
rs11265079	RAB13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158791000-158797400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:158791200-158797400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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