Variant report

Variant	rs9523304
Chromosome Location	chr13:91983910-91983911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:91980883..91984230-chr13:91997795..92000374,3	MCF-7	breast:
2	chr13:91983271..91985793-chr13:91995740..91997781,2	MCF-7	breast:
3	chr13:91979501..91981445-chr13:91981674..91984085,3	K562	blood:
4	chr13:91974112..91976391-chr13:91980920..91984576,5	K562	blood:

Variant related genes	Relation type
ENSG00000215417	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1330062	0.91[ASN][1000 genomes]
rs1330063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs3759452	0.84[GIH][hapmap]
rs4142965	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4284505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773624	0.95[ASN][1000 genomes]
rs4773625	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7319045	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7319759	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320878	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7322734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7324173	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336610	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8001004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8002779	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs932910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9515919	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9523307	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9523310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9523312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9523313	0.95[ASN][1000 genomes]
rs976547	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1943 gene(s)	inside rSNPs	diseases
7	nsv510620	chr13:91945174-91997422	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
8	esv1794000	chr13:91983910-92001350	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	esv1797111	chr13:91983910-92001472	Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9523304	GPC5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:91983000-91984200	Flanking Active TSS	GM12878-XiMat	blood
2	chr13:91983600-91984200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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