Variant report

Variant	rs4148005
Chromosome Location	chr17:66882466-66882467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66881632..66883175-chr17:66886048..66888951,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10852765	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11077801	0.84[ASN][1000 genomes]
rs1156340	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11651365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12451990	0.94[ASN][1000 genomes]
rs12452031	0.85[ASN][1000 genomes]
rs12952511	0.94[ASN][1000 genomes]
rs1373067	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1373068	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34952002	0.86[ASN][1000 genomes]
rs35241984	0.89[ASN][1000 genomes]
rs3744492	0.96[ASN][1000 genomes]
rs3744493	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3744494	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3744495	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3744496	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3826429	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4147313	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147314	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147998	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4147999	0.87[ASN][1000 genomes]
rs4148000	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4148002	0.96[ASN][1000 genomes]
rs4148004	0.87[ASN][1000 genomes]
rs4148008	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968824	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs4968825	0.86[ASN][1000 genomes]
rs4968968	0.88[ASN][1000 genomes]
rs4968970	0.87[ASN][1000 genomes]
rs4968971	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4968972	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4968973	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs61303445	0.87[ASN][1000 genomes]
rs6501834	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs66588031	0.87[ASN][1000 genomes]
rs66600020	0.87[ASN][1000 genomes]
rs67040494	0.94[ASN][1000 genomes]
rs67927198	0.87[ASN][1000 genomes]
rs68027451	0.87[ASN][1000 genomes]
rs7503035	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8065105	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8071218	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs8074603	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs8074769	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs991209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs991210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv908695	chr17:66865583-66904001	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv1061151	chr17:66881617-66973917	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4148005	ABCA8	cis	cerebellum	SCAN
rs4148005	ABCA8	cis	parietal	SCAN
rs4148005	PECAM1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66866800-66883600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr17:66869800-66883400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:66876200-66882600	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:66877000-66883800	Strong transcription	Adipose Nuclei	Adipose
6	chr17:66877000-66884000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr17:66877000-66886200	Weak transcription	Colonic Mucosa	Colon
8	chr17:66877000-66886600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr17:66877000-66889000	Weak transcription	Spleen	Spleen
10	chr17:66877000-66906200	Weak transcription	Fetal Stomach	stomach
11	chr17:66877200-66882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:66877200-66887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:66877400-66882600	Weak transcription	Placenta	Placenta
14	chr17:66877600-66888400	Strong transcription	Liver	Liver
15	chr17:66877600-66893400	Weak transcription	Brain Anterior Caudate	brain
16	chr17:66877800-66918200	Weak transcription	Fetal Brain Male	brain
17	chr17:66878200-66889400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr17:66878200-66899200	Weak transcription	Osteobl	bone
19	chr17:66878400-66901000	Weak transcription	Brain Angular Gyrus	brain
20	chr17:66879800-66892600	Weak transcription	Fetal Muscle Leg	muscle
21	chr17:66879800-66897000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:66880000-66893400	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:66880800-66883800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:66881000-66903200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:66881200-66893400	Weak transcription	Brain Substantia Nigra	brain
26	chr17:66881200-66904200	Weak transcription	Psoas Muscle	Psoas
27	chr17:66881400-66892800	Weak transcription	Fetal Heart	heart
28	chr17:66881400-66893600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr17:66881400-66893800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:66881400-66898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:66881400-66906400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr17:66881400-66906400	Weak transcription	Right Ventricle	heart
33	chr17:66881600-66882800	Weak transcription	Fetal Lung	lung
34	chr17:66881600-66893000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr17:66881800-66883200	Weak transcription	Ovary	ovary
36	chr17:66882000-66897600	Weak transcription	Left Ventricle	heart
37	chr17:66882400-66883000	Enhancers	HUVEC	blood vessel
38	chr17:66882400-66883800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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