Variant report

Variant	rs2002453
Chromosome Location	chr11:113289298-113289299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1003641	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1076560	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs1076562	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1079597	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs1079727	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs11214598	0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs11214602	0.92[ASN][1000 genomes]
rs1124493	0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1125393	0.91[CHD][hapmap]
rs17115583	0.87[JPT][hapmap]
rs2005313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075654	0.83[CHB][hapmap]
rs2242592	0.93[ASN][1000 genomes]
rs2245805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283265	0.83[CHB][hapmap]
rs2471850	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2471854	0.91[CHD][hapmap]
rs2471856	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471857	0.91[CHD][hapmap]
rs2511521	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587550	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2587552	0.92[ASN][1000 genomes]
rs2734841	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2734842	0.93[ASN][1000 genomes]
rs2859543	0.92[ASN][1000 genomes]
rs2859544	0.92[ASN][1000 genomes]
rs2859545	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4436578	0.87[JPT][hapmap]
rs4586205	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4620755	0.87[JPT][hapmap]
rs4648318	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4938016	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6275	0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs6276	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6279	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7122228	0.90[ASN][1000 genomes]
rs7125415	0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2002453	FDX1	cis	parietal	SCAN
rs2002453	TTC12	cis	lesional skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113278600-113300200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:113279000-113290600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:113285200-113291000	Weak transcription	Spleen	Spleen
4	chr11:113287800-113295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:113289000-113291600	Enhancers	Brain Germinal Matrix	brain

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