Variant report

Variant	rs11727923
Chromosome Location	chr4:76342004-76342005
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10518140	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs11099539	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11099546	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11722278	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs11727259	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727982	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11729106	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs11731477	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732511	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs12644911	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1351094	1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17278571	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1904104	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2126854	1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap]
rs2867919	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28785287	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903701	0.92[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs34868796	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57275697	0.93[EUR][1000 genomes]
rs6845472	1.00[CEU][hapmap]
rs6847297	0.95[EUR][1000 genomes]
rs6851699	0.95[EUR][1000 genomes]
rs7683530	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998511	chr4:76184807-76398377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2763368	chr4:76190070-76387413	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv461557	chr4:76212995-76363477	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv594688	chr4:76212995-76363477	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11727923	THAP6	cis	lymphoblastoid	seeQTL
rs11727923	THAP6	cis	Lymphoblastoid	GTEx
rs11727923	THAP6	cis	multi-tissue	Pritchard
rs11727923	RCHY1	cis	cerebellum	SCAN
rs11727923	RCHY1	cis	lymphoblastoid	seeQTL
rs11727923	RCHY1	cis	parietal	SCAN
rs11727923	RCHY1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76340600-76343000	Weak transcription	Fetal Heart	heart

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