Variant report

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11162433	0.93[CEU][hapmap]
rs11162435	0.81[ASN][1000 genomes]
rs11162436	0.81[ASN][1000 genomes]
rs1323097	0.81[ASN][1000 genomes]
rs1323099	0.81[ASN][1000 genomes]
rs1745624	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2181453	0.81[ASN][1000 genomes]
rs4650639	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs589683	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs591206	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs614836	0.86[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs637650	0.98[ASN][1000 genomes]
rs646971	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648315	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661630	0.82[EUR][1000 genomes]
rs6665090	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666897	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs679843	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs720579	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7540033	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs942100	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs681907	NEXN	cis	lymphoblastoid	seeQTL
rs681907	DNAJB4	cis	parietal	SCAN
rs681907	LHX8	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78689400-78692200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:78689600-78692800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:78689800-78692400	Enhancers	Liver	Liver
4	chr1:78689800-78697800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:78689800-78702400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:78689800-78703000	Weak transcription	Pancreas	Pancrea
7	chr1:78690200-78692600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:78690800-78693600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:78691400-78694000	Weak transcription	Hela-S3	cervix
10	chr1:78691800-78693400	Enhancers	Fetal Muscle Leg	muscle
11	chr1:78692000-78692200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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