Variant report

Variant	rs8068204
Chromosome Location	chr17:66897540-66897541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1373066	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1443259	0.86[AMR][1000 genomes]
rs1443261	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1443262	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1470292	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1470293	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1470294	0.86[AMR][1000 genomes]
rs1481	0.96[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs17742923	1.00[CHD][hapmap]
rs1838100	0.86[AMR][1000 genomes]
rs1838101	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1867235	0.81[AMR][1000 genomes]
rs2083790	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2218350	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2363753	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4246431	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4968826	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4968962	0.81[AMR][1000 genomes]
rs4968967	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6501766	0.81[AMR][1000 genomes]
rs6501767	0.81[AMR][1000 genomes]
rs6501768	0.81[AMR][1000 genomes]
rs6501813	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6501835	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6501839	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7209220	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7210022	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211979	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7216817	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8074944	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8080098	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8082619	0.86[AMR][1000 genomes]
rs894593	0.81[AMR][1000 genomes]
rs894594	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980423	0.86[AMR][1000 genomes]
rs9895868	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
6	nsv908696	chr17:66885526-66903293	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv908697	chr17:66885526-66913936	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv908698	chr17:66885526-66915598	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv908699	chr17:66885526-66933003	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv908700	chr17:66885526-66985992	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv908701	chr17:66888346-66978319	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv575928	chr17:66894861-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv1066412	chr17:66897540-66954067	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8068204	ABCA9	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr17:66877000-66906200	Weak transcription	Fetal Stomach	stomach
3	chr17:66877800-66918200	Weak transcription	Fetal Brain Male	brain
4	chr17:66878200-66899200	Weak transcription	Osteobl	bone
5	chr17:66878400-66901000	Weak transcription	Brain Angular Gyrus	brain
6	chr17:66881000-66903200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr17:66881200-66904200	Weak transcription	Psoas Muscle	Psoas
8	chr17:66881400-66898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:66881400-66906400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:66881400-66906400	Weak transcription	Right Ventricle	heart
11	chr17:66882000-66897600	Weak transcription	Left Ventricle	heart
12	chr17:66893000-66905200	Weak transcription	Fetal Muscle Leg	muscle
13	chr17:66893200-66906400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr17:66893400-66897600	Weak transcription	Ovary	ovary
15	chr17:66893400-66906400	Weak transcription	Fetal Heart	heart
16	chr17:66894000-66901600	Strong transcription	Fetal Lung	lung
17	chr17:66894000-66904400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr17:66894400-66898200	Weak transcription	Adipose Nuclei	Adipose
19	chr17:66894400-66899200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr17:66894800-66898200	Weak transcription	Brain Substantia Nigra	brain
21	chr17:66895600-66901600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:66896000-66903000	Strong transcription	Liver	Liver
23	chr17:66896600-66906200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:66896800-66897600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:66897000-66897600	Strong transcription	Brain Hippocampus Middle	brain
26	chr17:66897200-66898000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:66897200-66898200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:66897200-66901400	Weak transcription	Brain Anterior Caudate	brain
29	chr17:66897200-66902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr17:66897400-66898200	Weak transcription	Muscle Satellite Cultured Cells	--

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