Variant report

Variant	rs7211979
Chromosome Location	chr17:66899261-66899262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1373066	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1443259	0.88[AMR][1000 genomes]
rs1443261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1443262	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1470292	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1470293	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1470294	0.88[AMR][1000 genomes]
rs1481	0.96[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs17742923	1.00[CHD][hapmap]
rs1808919	0.81[AMR][1000 genomes]
rs1838100	0.88[AMR][1000 genomes]
rs1838101	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1867235	0.83[AMR][1000 genomes]
rs2083790	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2218350	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2363753	0.96[EUR][1000 genomes]
rs4246431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4968826	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4968962	0.83[AMR][1000 genomes]
rs4968967	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6501766	0.83[AMR][1000 genomes]
rs6501767	0.83[AMR][1000 genomes]
rs6501768	0.83[AMR][1000 genomes]
rs6501813	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6501835	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6501839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7209220	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7210022	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7216817	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068204	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]
rs8074944	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8080098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8082619	0.88[AMR][1000 genomes]
rs894593	0.83[AMR][1000 genomes]
rs894594	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980423	0.88[AMR][1000 genomes]
rs9895868	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
14	esv1846502	chr17:66899261-66966274	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1849165	chr17:66899261-66978319	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7211979	ABCA9	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr17:66878400-66901000	Weak transcription	Brain Angular Gyrus	brain
5	chr17:66881000-66903200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:66881200-66904200	Weak transcription	Psoas Muscle	Psoas
7	chr17:66881400-66906400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr17:66881400-66906400	Weak transcription	Right Ventricle	heart
9	chr17:66893000-66905200	Weak transcription	Fetal Muscle Leg	muscle
10	chr17:66893200-66906400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr17:66893400-66906400	Weak transcription	Fetal Heart	heart
12	chr17:66894000-66901600	Strong transcription	Fetal Lung	lung
13	chr17:66894000-66904400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:66895600-66901600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:66896000-66903000	Strong transcription	Liver	Liver
16	chr17:66896600-66906200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:66897200-66901400	Weak transcription	Brain Anterior Caudate	brain
18	chr17:66897200-66902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:66897600-66899600	Strong transcription	Left Ventricle	heart
20	chr17:66897600-66899600	Strong transcription	Ovary	ovary
21	chr17:66897600-66902000	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:66897600-66902600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:66898000-66900200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:66898000-66905200	Weak transcription	K562	blood
25	chr17:66898200-66899600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr17:66898200-66899800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:66898200-66902200	Strong transcription	Adipose Nuclei	Adipose
28	chr17:66898800-66899600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:66899000-66901800	Weak transcription	Small Intestine	intestine
30	chr17:66899000-66906200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:66899200-66899800	Genic enhancers	Brain Cingulate Gyrus	brain
32	chr17:66899200-66899800	Strong transcription	Osteobl	bone
33	chr17:66899200-66900000	Genic enhancers	Brain Substantia Nigra	brain

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