Variant report

Variant	rs534429
Chromosome Location	chr13:96734331-96734332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96732215..96734781-chr13:96740954..96743608,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185352	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10508027	0.88[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs11616724	0.81[AMR][1000 genomes]
rs11618108	0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs12428062	0.88[CEU][hapmap]
rs1327640	0.85[AMR][1000 genomes]
rs1854174	0.82[AMR][1000 genomes]
rs1854758	0.88[CEU][hapmap]
rs2129006	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2170813	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2257397	0.82[AMR][1000 genomes]
rs2257398	0.84[AMR][1000 genomes]
rs2262077	0.82[AMR][1000 genomes]
rs2849439	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4547219	0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs475882	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs490753	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs492247	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs492744	0.82[AMR][1000 genomes]
rs493423	0.89[AMR][1000 genomes]
rs495214	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs502311	0.85[AMR][1000 genomes]
rs504340	0.85[AMR][1000 genomes]
rs525770	0.89[EUR][1000 genomes]
rs526381	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs526702	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs531432	0.83[EUR][1000 genomes]
rs534010	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs539293	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs540213	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs543775	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs544815	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs547858	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs549594	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562879	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs564075	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs565297	0.86[CEU][hapmap]
rs565851	1.00[CEU][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs565898	0.88[CEU][hapmap]
rs568170	0.89[AMR][1000 genomes]
rs568945	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs571059	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573909	0.82[AMR][1000 genomes]
rs581462	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs593806	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602540	0.82[AMR][1000 genomes]
rs626317	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs627074	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs634236	0.89[EUR][1000 genomes]
rs639527	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs643302	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs645595	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs647811	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6492832	0.84[AMR][1000 genomes]
rs6492833	0.83[AMR][1000 genomes]
rs6492834	0.85[AMR][1000 genomes]
rs649322	0.81[AMR][1000 genomes]
rs658705	0.83[AMR][1000 genomes]
rs661544	0.87[EUR][1000 genomes]
rs662884	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs672988	0.85[AMR][1000 genomes]
rs674565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675144	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680576	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs680676	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs684902	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs686672	0.86[AMR][1000 genomes]
rs688133	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7139605	0.87[AMR][1000 genomes]
rs72637833	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72637836	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72637837	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7318247	0.82[AMR][1000 genomes]
rs7318449	0.85[AMR][1000 genomes]
rs7330650	0.85[AMR][1000 genomes]
rs7332078	0.89[CEU][hapmap]
rs7338171	0.85[AMR][1000 genomes]
rs7999737	0.88[CEU][hapmap]
rs816109	0.82[AMR][1000 genomes]
rs816122	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs816142	1.00[CEU][hapmap]
rs9516621	0.88[CEU][hapmap]
rs9516625	0.89[CEU][hapmap]
rs9525079	0.88[CEU][hapmap]
rs9525134	0.83[AMR][1000 genomes]
rs9525136	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs534429	GPC5	cis	parietal	SCAN
rs534429	DZIP1	cis	parietal	SCAN
rs534429	UGGT2	cis	cerebellum	SCAN
rs534429	UGCGL2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96733400-96735000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:96733800-96735000	Enhancers	Fetal Intestine Large	intestine
3	chr13:96734200-96734600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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