Variant report

Variant	rs11125179
Chromosome Location	chr2:48915871-48915872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10198501	0.80[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs10208754	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]
rs10495955	0.89[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs11125178	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11685904	0.89[CHD][hapmap]
rs11691408	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11892581	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11899239	0.81[AMR][1000 genomes]
rs11901588	0.82[CHB][hapmap]
rs12473064	0.82[AMR][1000 genomes]
rs12713012	1.00[CHB][hapmap]
rs12997569	0.89[CHD][hapmap]
rs13022553	1.00[CHB][hapmap]
rs13022734	0.80[AMR][1000 genomes]
rs13024367	1.00[CHB][hapmap]
rs1404051	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1464727	0.85[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1464729	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap]
rs1524148	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1524155	0.85[CEU][hapmap];0.87[AMR][1000 genomes]
rs1589749	0.89[CHD][hapmap]
rs17326209	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17326251	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1916838	1.00[CHB][hapmap]
rs1996968	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1996969	1.00[CHD][hapmap]
rs2056581	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2103113	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2293275	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2349099	0.89[CHD][hapmap]
rs2349101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28666758	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34378457	0.85[ASN][1000 genomes]
rs34757099	0.95[ASN][1000 genomes]
rs34790224	0.90[ASN][1000 genomes]
rs3792241	0.97[GIH][hapmap];0.81[EUR][1000 genomes]
rs3792243	0.89[CHD][hapmap]
rs3792246	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3811516	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62137532	0.90[ASN][1000 genomes]
rs6545051	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6545054	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6730379	1.00[CHB][hapmap]
rs6738387	0.89[CHD][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs6741840	1.00[CHB][hapmap]
rs6746530	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6746623	1.00[CHB][hapmap]
rs6747475	1.00[CHB][hapmap]
rs7583310	0.80[ASN][1000 genomes]
rs7587112	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11125179	STON1-GTF2A1L	cis	parietal	SCAN
rs11125179	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48863000-48919600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:48874200-48919600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:48898800-48920200	Weak transcription	Ovary	ovary
4	chr2:48908000-48920000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:48915400-48916000	Strong transcription	Adipose Nuclei	Adipose

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