Variant report

Variant	rs56049502
Chromosome Location	chr12:75927767-75927768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75925641..75928428-chr12:76424278..76425852,2	K562	blood:
2	chr12:75926063..75928483-chr12:75932746..75935493,2	MCF-7	breast:
3	chr12:75923131..75928282-chr12:76423369..76427377,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257839	Chromatin interaction
ENSG00000257453	Chromatin interaction
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11180552	0.81[ASN][1000 genomes]
rs11180560	1.00[ASN][1000 genomes]
rs11355	0.81[ASN][1000 genomes]
rs1147995	0.98[ASN][1000 genomes]
rs1147997	0.98[ASN][1000 genomes]
rs11540407	0.81[ASN][1000 genomes]
rs11610328	1.00[ASN][1000 genomes]
rs11611609	0.81[ASN][1000 genomes]
rs11830640	0.94[ASN][1000 genomes]
rs12811160	0.98[ASN][1000 genomes]
rs12812559	0.81[ASN][1000 genomes]
rs12815116	0.81[ASN][1000 genomes]
rs12819511	0.81[ASN][1000 genomes]
rs12822493	0.97[ASN][1000 genomes]
rs12826635	0.81[ASN][1000 genomes]
rs12827668	0.81[ASN][1000 genomes]
rs12827986	0.97[ASN][1000 genomes]
rs1290026	0.97[ASN][1000 genomes]
rs1383100	0.94[ASN][1000 genomes]
rs1501634	0.81[ASN][1000 genomes]
rs15513	0.81[ASN][1000 genomes]
rs1552039	0.81[ASN][1000 genomes]
rs1604381	0.81[ASN][1000 genomes]
rs17218895	0.81[ASN][1000 genomes]
rs17220228	0.98[ASN][1000 genomes]
rs17818307	0.81[ASN][1000 genomes]
rs1824981	0.92[ASN][1000 genomes]
rs2054517	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2070162	0.81[ASN][1000 genomes]
rs2279244	0.81[ASN][1000 genomes]
rs2306391	0.81[ASN][1000 genomes]
rs2700521	0.97[ASN][1000 genomes]
rs34170388	0.98[ASN][1000 genomes]
rs35619460	0.81[ASN][1000 genomes]
rs35708464	0.98[ASN][1000 genomes]
rs3741495	0.81[ASN][1000 genomes]
rs3809121	0.81[ASN][1000 genomes]
rs3847672	0.97[ASN][1000 genomes]
rs3847673	0.97[ASN][1000 genomes]
rs56222143	0.98[ASN][1000 genomes]
rs61933362	0.81[ASN][1000 genomes]
rs61933387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933428	0.89[AMR][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	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56049502	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75927000-75928200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr12:75927200-75928600	Enhancers	HSMMtube	muscle

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