Variant report

Variant	rs2054516
Chromosome Location	chr12:76037103-76037104
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76036220..76038059-chr12:76047877..76049953,2	MCF-7	breast:
2	chr12:75953077..75955881-chr12:76035661..76037808,2	MCF-7	breast:
3	chr12:76032186..76035156-chr12:76036962..76040307,4	K562	blood:
4	chr12:76036874..76039310-chr12:76041126..76043047,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10785198	0.81[ASN][1000 genomes]
rs10879936	0.86[ASN][1000 genomes]
rs10879949	0.99[ASN][1000 genomes]
rs11180598	0.90[ASN][1000 genomes]
rs11180603	0.86[ASN][1000 genomes]
rs11519910	0.81[ASN][1000 genomes]
rs11520226	0.81[ASN][1000 genomes]
rs2366989	0.87[ASN][1000 genomes]
rs2886828	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4882635	0.81[ASN][1000 genomes]
rs58886425	0.88[ASN][1000 genomes]
rs60465677	0.82[ASN][1000 genomes]
rs6582293	0.90[ASN][1000 genomes]
rs6582294	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137610	0.93[ASN][1000 genomes]
rs7297580	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305673	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7314220	0.81[ASN][1000 genomes]
rs7315474	0.96[ASN][1000 genomes]
rs7956673	0.97[ASN][1000 genomes]
rs7956953	0.88[ASN][1000 genomes]
rs7958508	0.83[ASN][1000 genomes]
rs7962144	0.93[ASN][1000 genomes]
rs7962276	0.96[ASN][1000 genomes]
rs7979460	0.88[ASN][1000 genomes]
rs7979600	0.82[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2054516	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs2054516	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs2054516	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs2054516	GLIPR1L2	cis	Artery Tibial	GTEx
rs2054516	GLIPR1L2	cis	Thyroid	GTEx
rs2054516	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs2054516	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs2054516	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2054516	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs2054516	GLIPR1L2	cis	Nerve Tibial	GTEx
rs2054516	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs2054516	GLIPR1L2	cis	lung	GTEx
rs2054516	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs2054516	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs2054516	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs2054516	RP11-585P4.5	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76032400-76037200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:76034600-76037200	Enhancers	NH-A	brain
3	chr12:76035400-76037200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:76035400-76038000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:76035400-76040200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:76035600-76037800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:76035600-76038000	Enhancers	GM12878-XiMat	blood
8	chr12:76035600-76038400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:76035600-76039800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:76035600-76042400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:76035600-76044600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:76035600-76050400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:76035800-76037800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:76035800-76044800	Weak transcription	K562	blood
15	chr12:76036400-76038000	Weak transcription	Dnd41	blood
16	chr12:76036600-76040200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:76036600-76040200	Weak transcription	HSMMtube	muscle
18	chr12:76036600-76044000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:76036600-76044400	Weak transcription	NHEK	skin
20	chr12:76036800-76040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:76036800-76042600	Weak transcription	HMEC	breast
22	chr12:76036800-76044400	Weak transcription	NHDF-Ad	bronchial
23	chr12:76036800-76045000	Weak transcription	HSMM	muscle
24	chr12:76036800-76050000	Weak transcription	NHLF	lung

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