Variant report

Variant	rs12299578
Chromosome Location	chr12:75981353-75981354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10785197	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180559	0.91[ASN][1000 genomes]
rs11180576	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180577	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180591	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180592	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1147994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1351328	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1383098	0.99[ASN][1000 genomes]
rs1383101	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1480001	0.99[ASN][1000 genomes]
rs1480002	0.99[ASN][1000 genomes]
rs1542570	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552040	0.90[ASN][1000 genomes]
rs1611928	0.96[ASN][1000 genomes]
rs1627431	0.99[ASN][1000 genomes]
rs1630753	0.97[ASN][1000 genomes]
rs1679380	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1697753	0.99[ASN][1000 genomes]
rs1795374	0.98[ASN][1000 genomes]
rs1795380	0.99[ASN][1000 genomes]
rs1795382	0.99[ASN][1000 genomes]
rs2620687	0.99[ASN][1000 genomes]
rs2652022	0.99[ASN][1000 genomes]
rs3912214	0.95[ASN][1000 genomes]
rs4882638	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56904707	0.91[ASN][1000 genomes]
rs57091991	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7297463	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73185062	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960251	0.99[EUR][1000 genomes];1.00[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
rs12299578	GLIPR1L2	cis	parietal	SCAN
rs12299578	ATXN7L3B	cis	cerebellum	SCAN
rs12299578	GLIPR1L2	cis	cerebellum	SCAN
rs12299578	E2F7	cis	parietal	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	chr12:75980000-75981400	Weak transcription	NH-A	brain
6	chr12:75980000-75983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:75980000-75983200	Weak transcription	NHLF	lung
8	chr12:75980000-75985400	Weak transcription	HSMMtube	muscle
9	chr12:75980000-76017000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:75980200-75981400	Weak transcription	Osteobl	bone
11	chr12:75981000-75982000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:75981200-75981400	Enhancers	Aorta	Aorta
13	chr12:75981200-75981400	Enhancers	HMEC	breast
14	chr12:75981200-75981600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:75981200-75981600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:75981200-75981800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:75981200-75982200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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