Variant report

Variant	rs2125204
Chromosome Location	chr3:28557938-28557939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10460987	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10510611	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12054402	0.93[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap]
rs13100556	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[ASN][1000 genomes]
rs2371302	0.91[ASN][1000 genomes]
rs35447037	0.83[ASN][1000 genomes]
rs35714039	0.98[ASN][1000 genomes]
rs4234347	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4680751	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[ASN][1000 genomes]
rs4680756	0.80[ASN][1000 genomes]
rs6762982	0.84[ASN][1000 genomes]
rs6764496	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs6781639	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6797502	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6805743	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72909081	0.96[ASN][1000 genomes]
rs72909087	0.92[ASN][1000 genomes]
rs72911006	0.93[ASN][1000 genomes]
rs72911030	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72911060	0.80[ASN][1000 genomes]
rs7619946	0.95[ASN][1000 genomes]
rs7633509	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv876650	chr3:28427029-28613602	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1015015	chr3:28461972-28728494	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv916364	chr3:28468275-29146280	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv590010	chr3:28469830-28727214	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1004457	chr3:28541307-28595311	Strong transcription Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2125204	STAT4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28514800-28575800	Weak transcription	Ovary	ovary
2	chr3:28547200-28559800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:28557800-28558200	Enhancers	HUES48 Cell Line	embryonic stem cell

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