Variant report

Variant	rs2721123
Chromosome Location	chr11:18475100-18475101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18474174..18475881-chr11:18477733..18480422,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10766473	0.82[CHD][hapmap]
rs10766475	1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs10766478	0.83[ASN][1000 genomes]
rs10832927	0.95[CHB][hapmap];0.86[AMR][1000 genomes]
rs10832929	0.85[AMR][1000 genomes]
rs10832930	0.85[AMR][1000 genomes]
rs10832931	0.85[AMR][1000 genomes]
rs10832932	0.85[AMR][1000 genomes]
rs10832933	0.85[AMR][1000 genomes]
rs11024636	0.82[CHD][hapmap]
rs1830426	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs1881716	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs1881717	0.83[CHB][hapmap]
rs1969562	0.85[AMR][1000 genomes]
rs1969563	0.85[AMR][1000 genomes]
rs2249631	0.88[AMR][1000 genomes]
rs2403278	0.82[CHD][hapmap]
rs2403279	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs2658566	0.83[CHB][hapmap]
rs2698564	0.84[ASN][1000 genomes]
rs3758680	0.95[CHB][hapmap];0.85[AMR][1000 genomes]
rs3758681	0.82[CHD][hapmap]
rs3758682	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs3781641	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs3809096	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs4274186	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs5030621	0.85[AMR][1000 genomes]
rs6486425	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs7106099	0.95[CHB][hapmap];0.86[AMR][1000 genomes]
rs7111748	1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs7112492	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs7120485	0.85[AMR][1000 genomes]
rs7121244	0.95[CHB][hapmap];0.85[AMR][1000 genomes]
rs7128549	0.95[CHB][hapmap];0.85[AMR][1000 genomes]
rs7129689	0.82[CHD][hapmap]
rs7130990	0.83[AMR][1000 genomes]
rs7938942	0.95[JPT][hapmap]
rs7947664	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv897027	chr11:18435700-18499416	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	esv3393833	chr11:18471936-18480010	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2721123	COPB1	cis	cerebellum	SCAN
rs2721123	LDHC	cis	Artery Tibial	GTEx
rs2721123	LDHAL6A	cis	parietal	SCAN
rs2721123	LDHC	cis	lymphoblastoid	seeQTL
rs2721123	LDHC	cis	Muscle Skeletal	GTEx
rs2721123	TSG101	cis	lymphoblastoid	seeQTL
rs2721123	LDHC	cis	Nerve Tibial	GTEx
rs2721123	LDHC	cis	lung	GTEx
rs2721123	LDHC	cis	parietal	SCAN
rs2721123	LDHC	cis	Thyroid	GTEx
rs2721123	LDHA	cis	cerebellum	SCAN
rs2721123	LDHC	cis	cerebellum	SCAN
rs2721123	LDHAL6A	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18457200-18479200	Weak transcription	Pancreas	Pancrea
2	chr11:18475000-18476000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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