Variant report

Variant	rs494052
Chromosome Location	chr1:153139037-153139038
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	chr1:153138048..153140059-chr17:57914589..57916677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12403746	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12403764	0.88[EUR][1000 genomes]
rs12406257	0.89[EUR][1000 genomes]
rs12744123	0.96[EUR][1000 genomes]
rs1625198	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1697430	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1697431	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2455009	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs473096	0.99[EUR][1000 genomes]
rs474200	0.94[EUR][1000 genomes]
rs474907	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs475182	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475698	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs476761	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs478641	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs488552	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs499893	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs503914	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs509194	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs510277	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs524887	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531073	0.83[EUR][1000 genomes]
rs531103	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs533437	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs547119	0.96[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs550463	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553175	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555926	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs556824	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557982	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564787	1.00[CEU][hapmap]
rs575860	0.98[ASN][1000 genomes]
rs576035	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][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	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1004168	chr1:153088209-153226033	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1013041	chr1:153105260-153223716	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv946347	chr1:153138813-153140659	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs494052	PGLYRP4	cis	parietal	SCAN
rs494052	LELP1	cis	parietal	SCAN
rs494052	PBXIP1	cis	parietal	SCAN
rs494052	ASH1L	cis	parietal	SCAN
rs494052	LCE3B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153138400-153141400	Weak transcription	H9 Cell Line	embryonic stem cell

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