Variant report

Variant	rs11731477
Chromosome Location	chr4:76359426-76359427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76358069..76359586-chr4:76396767..76398904,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RCHY1-1	chr4:76359328-76359659	XLOC_003988

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

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];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs11099539	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11099546	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11722278	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs11727259	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11727923	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727982	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11729106	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs11732511	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs12644911	0.87[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];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17278571	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904104	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2126854	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap]
rs2867919	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28785287	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2903701	0.92[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs34868796	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57275697	0.93[EUR][1000 genomes]
rs6845472	1.00[CEU][hapmap]
rs6847297	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6851699	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7683530	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv822619	chr4:76351246-76359789	Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11731477	RCHY1	cis	cerebellum	SCAN
rs11731477	THAP6	cis	Lymphoblastoid	GTEx
rs11731477	RCHY1	Cis_1M	lymphoblastoid	RTeQTL
rs11731477	THAP6	cis	multi-tissue	Pritchard
rs11731477	RCHY1	cis	parietal	SCAN
rs11731477	RCHY1	cis	lymphoblastoid	seeQTL
rs11731477	THAP6	cis	lymphoblastoid	seeQTL
rs11731477	RCHY1	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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