Variant report

Variant	rs1480001
Chromosome Location	chr12:75980719-75980720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10785197	0.94[ASN][1000 genomes]
rs10879928	0.85[GIH][hapmap]
rs11180559	0.90[ASN][1000 genomes]
rs11180576	0.99[ASN][1000 genomes]
rs11180577	0.97[ASN][1000 genomes]
rs11180591	0.94[ASN][1000 genomes]
rs1147994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148003	0.85[AFR][1000 genomes]
rs1148005	0.88[CEU][hapmap]
rs1148006	0.83[CEU][hapmap]
rs12299578	0.99[ASN][1000 genomes]
rs1275474	0.85[GIH][hapmap]
rs1351328	0.96[ASN][1000 genomes]
rs1383098	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383101	0.88[ASN][1000 genomes]
rs1480002	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542570	0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1552040	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1611928	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1627431	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630753	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1679380	0.95[ASN][1000 genomes]
rs1697753	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795374	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795380	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795382	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620687	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652022	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847669	0.83[CEU][hapmap]
rs3912214	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882638	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs56904707	0.90[ASN][1000 genomes]
rs57091991	0.97[ASN][1000 genomes]
rs7297463	0.98[ASN][1000 genomes]
rs73185062	0.99[ASN][1000 genomes]
rs7960251	0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1480001	GLIPR1L2	cis	parietal	SCAN
rs1480001	GLIPR1	cis	cerebellum	SCAN
rs1480001	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs1480001	GLIPR1L2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75977600-75985200	Weak transcription	Fetal Brain Female	brain
2	chr12:75978400-75986800	Enhancers	NHDF-Ad	bronchial
3	chr12:75978600-75981600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:75979200-75981800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:75979400-75981200	Weak transcription	Aorta	Aorta
6	chr12:75979800-75981200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:75980000-75981000	Weak transcription	HMEC	breast
8	chr12:75980000-75981200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:75980000-75981200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:75980000-75981400	Weak transcription	NH-A	brain
11	chr12:75980000-75983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:75980000-75983200	Weak transcription	NHLF	lung
13	chr12:75980000-75985400	Weak transcription	HSMMtube	muscle
14	chr12:75980000-76017000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:75980200-75981400	Weak transcription	Osteobl	bone
16	chr12:75980600-75980800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:75980600-75981000	Weak transcription	Muscle Satellite Cultured Cells	--

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