Variant report

Variant	rs1925121
Chromosome Location	chr13:96938780-96938781
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96933248..96934803-chr13:96938522..96940997,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11069237	0.80[EUR][1000 genomes]
rs11841294	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327631	0.87[ASN][1000 genomes]
rs1327632	0.87[ASN][1000 genomes]
rs1815354	0.85[ASN][1000 genomes]
rs1925116	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925118	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927785	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1927786	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927789	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927791	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1927792	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927793	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1927794	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1927795	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927796	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1927800	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1927801	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1930221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1930222	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2147687	0.84[EUR][1000 genomes]
rs2149315	0.82[EUR][1000 genomes]
rs2183981	0.81[EUR][1000 genomes]
rs2389630	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4773947	0.82[EUR][1000 genomes]
rs4773948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334728	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7336212	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7337860	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs764574	0.89[ASN][1000 genomes]
rs7986153	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998759	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300341	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9513118	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9516652	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9525158	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9525170	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9525173	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9554335	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556537	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9556538	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9556541	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9590372	0.87[ASN][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	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv530742	chr13:96917313-97627023	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1925121	UGCGL2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96936800-96940200	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr13:96938400-96946000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:96938600-96946400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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