Variant report

Variant	rs56222143
Chromosome Location	chr12:75962721-75962722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75955678..75958303-chr12:75962611..75964917,2	MCF-7	breast:
2	chr12:75961478..75964130-chr12:75966131..75968035,2	K562	blood:
3	chr12:75961729..75963400-chr12:76429164..76431160,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11180560	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1147995	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147997	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610328	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830640	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12811160	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12822493	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12827986	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1290026	0.98[ASN][1000 genomes]
rs1383100	0.95[ASN][1000 genomes]
rs17220228	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2054517	0.98[ASN][1000 genomes]
rs2700521	0.98[ASN][1000 genomes]
rs34170388	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708464	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847672	0.98[ASN][1000 genomes]
rs3847673	0.98[ASN][1000 genomes]
rs56049502	0.98[ASN][1000 genomes]
rs61933387	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	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
rs56222143	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75954600-75964800	Weak transcription	Brain Substantia Nigra	brain
2	chr12:75958800-75965000	Weak transcription	Fetal Brain Female	brain
3	chr12:75959600-75963200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:75960200-75966000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:75961200-75963000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:75961200-75963400	Enhancers	Fetal Lung	lung
7	chr12:75961400-75963000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:75961400-75963000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:75961400-75963400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:75961600-75962800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:75961600-75963000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:75961600-75963000	Enhancers	Fetal Stomach	stomach
13	chr12:75961800-75962800	Enhancers	NHLF	lung
14	chr12:75961800-75963000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:75962000-75962800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:75962000-75962800	Bivalent Enhancer	Brain Germinal Matrix	brain
17	chr12:75962000-75962800	Enhancers	NH-A	brain
18	chr12:75962000-75962800	Enhancers	Osteobl	bone
19	chr12:75962200-75962800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:75962200-75962800	Enhancers	NHEK	skin
21	chr12:75962200-75963000	Enhancers	HMEC	breast
22	chr12:75962400-75962800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:75962400-75963000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:75962400-75963000	Enhancers	Fetal Heart	heart
25	chr12:75962600-75964000	Weak transcription	Brain Angular Gyrus	brain

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