Variant report

Variant	rs2054517
Chromosome Location	chr12:75991446-75991447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10506667	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180552	0.81[ASN][1000 genomes]
rs11180560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11355	0.81[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1147997	0.98[ASN][1000 genomes]
rs11540407	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11610328	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11611121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11830640	0.94[ASN][1000 genomes]
rs12811160	0.95[ASN][1000 genomes]
rs12812559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12815116	0.81[ASN][1000 genomes]
rs12819511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[ASN][1000 genomes]
rs12826635	0.81[ASN][1000 genomes]
rs12827668	0.81[ASN][1000 genomes]
rs12827986	1.00[ASN][1000 genomes]
rs1290026	0.97[ASN][1000 genomes]
rs1383100	0.97[ASN][1000 genomes]
rs1501634	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs15513	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1552039	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs1604381	0.81[ASN][1000 genomes]
rs17217158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17218895	0.81[ASN][1000 genomes]
rs17220228	0.98[ASN][1000 genomes]
rs17818307	0.81[ASN][1000 genomes]
rs1824981	0.90[ASN][1000 genomes]
rs2070162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2279244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2306391	1.00[CHB][hapmap];1.00[JPT][hapmap];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	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3809118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3809121	0.81[ASN][1000 genomes]
rs3847672	0.97[ASN][1000 genomes]
rs3847673	0.97[ASN][1000 genomes]
rs56049502	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56222143	0.98[ASN][1000 genomes]
rs61933362	0.81[ASN][1000 genomes]
rs61933387	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61933428	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2054517	GLIPR1L2	cis	cerebellum	SCAN
rs2054517	KRR1	cis	cerebellum	SCAN
rs2054517	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs2054517	GLIPR1L2	cis	parietal	SCAN
rs2054517	KRR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75980000-76017000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:75986800-75995200	Weak transcription	NHDF-Ad	bronchial
3	chr12:75991000-75992800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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