Variant report

Variant	rs1545755
Chromosome Location	chr19:37981509-37981510
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37980271..37981880-chr19:37996131..37997728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266916	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1019494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10419281	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10425719	0.92[CEU][hapmap];0.96[JPT][hapmap]
rs11083423	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11666708	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462546	0.94[ASN][1000 genomes]
rs12981359	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12981830	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs185368	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs185369	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs1968251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385180	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385181	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2431992	0.95[JPT][hapmap]
rs256733	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs256735	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs256740	0.81[ASN][1000 genomes]
rs256744	0.81[ASN][1000 genomes]
rs2927745	0.95[CHB][hapmap]
rs34410821	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35470250	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4344867	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502546	0.87[JPT][hapmap]
rs6508721	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508725	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247090	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7254009	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1545755	AC012309.5	cis	Esophagus Muscularis	GTEx
rs1545755	AC012309.5	cis	Thyroid	GTEx
rs1545755	AC012309.5	cis	Heart Left Ventricle	GTEx
rs1545755	AC012309.5	cis	Artery Tibial	GTEx
rs1545755	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37963800-37985600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37966200-37984000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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