Variant report

Variant	rs1567712
Chromosome Location	chr9:2660722-2660723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11788728	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789583	1.00[ASN][1000 genomes]
rs11790283	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791537	1.00[ASN][1000 genomes]
rs11793899	0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs11793901	1.00[ASN][1000 genomes]
rs13283954	1.00[ASN][1000 genomes]
rs17656379	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17712698	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs1869593	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947447	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889261	1.00[ASN][1000 genomes]
rs33955077	1.00[ASN][1000 genomes]
rs33984475	1.00[ASN][1000 genomes]
rs34318472	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34562568	1.00[ASN][1000 genomes]
rs35033160	1.00[ASN][1000 genomes]
rs35043989	1.00[ASN][1000 genomes]
rs35075133	1.00[ASN][1000 genomes]
rs35456336	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35730767	1.00[ASN][1000 genomes]
rs35769682	1.00[ASN][1000 genomes]
rs35847091	1.00[ASN][1000 genomes]
rs36036004	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6144	1.00[ASN][1000 genomes]
rs6145	0.82[GIH][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6148	0.88[GIH][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs6475888	0.82[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030221	1.00[ASN][1000 genomes]
rs7040916	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045124	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045363	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692565	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692571	1.00[ASN][1000 genomes]
rs72692574	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692579	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692580	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694628	1.00[ASN][1000 genomes]
rs7865617	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs8210	0.82[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970122	1.00[ASN][1000 genomes]
rs970123	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	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1567712	CCDC24	trans	parietal	SCAN
rs1567712	VLDLR	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2640000-2662200	Weak transcription	Right Atrium	heart
2	chr9:2641400-2668400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:2643800-2664000	Weak transcription	Spleen	Spleen
4	chr9:2643800-2666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:2644000-2667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:2649200-2664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:2653000-2666600	Weak transcription	Fetal Stomach	stomach
8	chr9:2653600-2662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:2653600-2664000	Weak transcription	Esophagus	oesophagus
10	chr9:2653800-2663600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:2653800-2663800	Weak transcription	Right Ventricle	heart
12	chr9:2654000-2662200	Weak transcription	Brain Substantia Nigra	brain
13	chr9:2654200-2666800	Weak transcription	Lung	lung
14	chr9:2654400-2663400	Weak transcription	Fetal Brain Male	brain
15	chr9:2655200-2664400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:2655600-2661600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:2655600-2662000	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:2655600-2662800	Weak transcription	Brain Anterior Caudate	brain
19	chr9:2655600-2664200	Weak transcription	Ovary	ovary
20	chr9:2655600-2664600	Weak transcription	Fetal Brain Female	brain
21	chr9:2655800-2661200	Weak transcription	HSMMtube	muscle
22	chr9:2655800-2662000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:2655800-2662200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:2655800-2663200	Weak transcription	Adipose Nuclei	Adipose
25	chr9:2655800-2664000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:2656000-2662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:2656000-2662800	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:2656000-2664000	Weak transcription	Pancreas	Pancrea
29	chr9:2656000-2666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:2656000-2677800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:2656200-2661600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:2656400-2661200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:2656400-2661200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:2656400-2664000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:2657000-2661200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:2657600-2661000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:2657800-2661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:2658800-2662200	Weak transcription	Left Ventricle	heart
39	chr9:2658800-2663600	Weak transcription	Dnd41	blood
40	chr9:2659800-2661200	Weak transcription	Fetal Heart	heart
41	chr9:2660200-2661200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:2660400-2661200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:2660400-2663200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:2660600-2662200	Weak transcription	Psoas Muscle	Psoas

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