Variant report

Variant	rs1552040
Chromosome Location	chr12:75922217-75922218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75919171..75922679-chr12:76098756..76100488,3	MCF-7	breast:
2	chr12:75918349..75922851-chr12:76423877..76426904,6	MCF-7	breast:
3	chr12:75921052..75923750-chr12:76434920..76437583,2	MCF-7	breast:
4	chr12:75918799..75923199-chr12:76423182..76427634,7	MCF-7	breast:

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

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10785197	0.85[ASN][1000 genomes]
rs10879928	0.83[AFR][1000 genomes]
rs11180559	0.99[ASN][1000 genomes]
rs11180576	0.90[ASN][1000 genomes]
rs11180577	0.89[ASN][1000 genomes]
rs11180591	0.85[ASN][1000 genomes]
rs1147994	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12299578	0.90[ASN][1000 genomes]
rs1351328	0.88[ASN][1000 genomes]
rs1383098	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1383101	0.80[ASN][1000 genomes]
rs1480001	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1480002	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1611928	0.89[ASN][1000 genomes]
rs1627431	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1630753	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1679380	0.86[ASN][1000 genomes]
rs1697753	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1795374	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1795379	0.81[AFR][1000 genomes]
rs1795380	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1795382	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2620687	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2652022	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3912214	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56904707	0.99[ASN][1000 genomes]
rs57091991	0.89[ASN][1000 genomes]
rs7297463	0.89[ASN][1000 genomes]
rs73185062	0.90[ASN][1000 genomes]
rs7960251	0.90[ASN][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
rs1552040	GLIPR1L2	cis	Muscle Skeletal	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75919400-75922800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:75920400-75922800	Enhancers	A549	lung
3	chr12:75920600-75924000	Enhancers	Fetal Lung	lung
4	chr12:75920800-75922400	Weak transcription	Fetal Heart	heart
5	chr12:75921000-75922600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:75921400-75922600	Enhancers	Fetal Brain Male	brain
7	chr12:75921600-75922600	Enhancers	Fetal Brain Female	brain
8	chr12:75921600-75922600	Enhancers	NHDF-Ad	bronchial
9	chr12:75921800-75922600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:75922000-75922400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:75922000-75922400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:75922200-75922400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:75922200-75922400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:75922200-75922400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr12:75922200-75922400	Enhancers	NH-A	brain
16	chr12:75922200-75922600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:75922200-75922800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:75922200-75922800	Enhancers	HSMMtube	muscle

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