Variant report

Variant	rs16870621
Chromosome Location	chr4:21244892-21244893
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10006105	0.89[CEU][hapmap]
rs10013976	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1023721	0.86[JPT][hapmap]
rs1023722	0.85[JPT][hapmap]
rs10516376	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516377	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs10938829	0.85[JPT][hapmap]
rs11943777	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11944859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs11944996	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs12640602	1.00[CEU][hapmap]
rs1425333	0.89[CEU][hapmap]
rs1425334	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1425336	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867638	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1834350	0.82[ASN][1000 genomes]
rs1865193	0.85[JPT][hapmap]
rs1967398	0.89[CEU][hapmap]
rs2162081	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]
rs28420737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4090720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448011	0.85[JPT][hapmap]
rs6448013	0.85[JPT][hapmap]
rs6823638	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6824763	0.85[JPT][hapmap]
rs6832734	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6858323	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73249506	0.82[ASN][1000 genomes]
rs73249509	0.82[ASN][1000 genomes]
rs73249518	0.88[ASN][1000 genomes]
rs7695878	0.85[JPT][hapmap]
rs9991408	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16870621	LCORL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21243200-21246600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:21244600-21246200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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