Variant report

Variant	rs2162081
Chromosome Location	chr4:21250060-21250061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10006105	0.89[CEU][hapmap]
rs10516376	0.89[CEU][hapmap]
rs10516377	0.89[CEU][hapmap]
rs11936275	0.89[CHD][hapmap]
rs11943777	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11944859	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs11944996	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap]
rs12640602	1.00[CEU][hapmap]
rs12648055	0.80[MEX][hapmap]
rs1425333	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs1425334	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1425336	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs16867638	0.89[CEU][hapmap];0.90[YRI][hapmap]
rs16870621	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs16870639	0.89[ASN][1000 genomes]
rs16870654	0.89[CHD][hapmap];0.80[MEX][hapmap]
rs1967398	0.89[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs28420737	0.85[AFR][1000 genomes]
rs28528979	0.80[AMR][1000 genomes]
rs28655062	0.85[AFR][1000 genomes]
rs4090720	0.85[AFR][1000 genomes]
rs59556101	0.89[ASN][1000 genomes]
rs6823638	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6832734	0.89[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6839686	0.86[CHD][hapmap];0.86[MEX][hapmap]
rs6839994	0.87[CHD][hapmap];0.80[MEX][hapmap]
rs6858323	0.82[ASW][hapmap];0.90[CEU][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9999019	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1002610	chr4:21192993-21261812	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	esv3341246	chr4:21248279-21250827	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv3375777	chr4:21248454-21250627	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
7	esv3468310	chr4:21248954-21250252	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
8	esv3468311	chr4:21248954-21250252	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2162081	LCORL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21249800-21250200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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