Variant report

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs34867472	0.97[ASN][1000 genomes]
rs3768190	0.81[MEX][hapmap]
rs472811	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs486736	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs493334	0.99[ASN][1000 genomes]
rs496780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs514550	0.82[MEX][hapmap]
rs516494	0.94[ASN][1000 genomes]
rs517051	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs517291	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs517412	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs517794	0.97[ASN][1000 genomes]
rs518258	0.99[ASN][1000 genomes]
rs521147	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs531729	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[YRI][hapmap];0.97[ASN][1000 genomes]
rs549528	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs559871	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs564616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs567862	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs570011	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs575163	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59491159	0.94[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs485090	LRP8	cis	parietal	SCAN
rs485090	HSPB11	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57534000-57552600	Weak transcription	Fetal Intestine Large	intestine
2	chr1:57544000-57555000	Weak transcription	Left Ventricle	heart
3	chr1:57548000-57553000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:57548000-57553400	Enhancers	Ovary	ovary
5	chr1:57548800-57553000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:57548800-57566600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:57549000-57555200	Weak transcription	Right Atrium	heart
8	chr1:57549200-57554600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:57549600-57556000	Weak transcription	Right Ventricle	heart
10	chr1:57549600-57566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:57550200-57555400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:57550400-57552600	Enhancers	Fetal Brain Male	brain
13	chr1:57550400-57553400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:57550800-57552600	Enhancers	Fetal Brain Female	brain
15	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:57552000-57553400	Enhancers	Fetal Heart	heart
17	chr1:57552200-57553000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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