Variant report

Variant	rs2468779
Chromosome Location	chr11:18245602-18245603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10766463	0.89[EUR][1000 genomes]
rs10832908	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs11024561	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024563	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11024578	0.88[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12364058	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs1378609	1.00[CHB][hapmap]
rs2168363	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2445145	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2445174	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2445175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2445176	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445218	0.86[AMR][1000 genomes]
rs2445225	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2445226	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460831	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2468789	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2468790	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2468856	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925145	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3100768	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4757628	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4757629	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4757630	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56310011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67006796	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67712345	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7103794	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7117484	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7117890	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7935726	0.82[AMR][1000 genomes];0.90[EUR][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv975156	chr11:18230807-18245674	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
4	esv3440516	chr11:18242376-18246674	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2468779	LDHC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18243400-18245800	Enhancers	HepG2	liver
2	chr11:18244600-18247000	Enhancers	Liver	Liver
3	chr11:18244800-18246400	Weak transcription	Spleen	Spleen
4	chr11:18245000-18246600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:18245600-18245800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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