Variant report

Variant	rs1559669
Chromosome Location	chr11:107084715-107084716
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10890666	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10890668	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1352735	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472078	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1490942	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1817798	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1834330	0.81[EUR][1000 genomes]
rs1844748	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844750	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1863260	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1863261	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1907403	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1991197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2017907	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059462	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098846	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2130823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194844	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2883480	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4265572	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4753787	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4754200	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs512574	0.81[MEX][hapmap]
rs559269	1.00[YRI][hapmap]
rs6588950	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102140	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7106065	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7108632	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7927069	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932525	0.90[AMR][1000 genomes]
rs7935653	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936174	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7936346	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7946110	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs962380	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531938	chr11:106760733-107156814	Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv898364	chr11:106944975-107285636	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv832260	chr11:106975094-107181795	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv556279	chr11:107006900-107186896	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1035911	chr11:107020991-107198181	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1040190	chr11:107045534-107175661	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv898371	chr11:107049968-107130964	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1559669	CARD17	cis	cerebellum	SCAN
rs1559669	DDX10	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107081000-107085800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:107081000-107089200	Weak transcription	Fetal Brain Male	brain
3	chr11:107084400-107084800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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