Variant report

Variant	rs6501839
Chromosome Location	chr17:66883719-66883720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1443259	0.97[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1443262	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1470292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1470293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1470294	0.97[AMR][1000 genomes]
rs1481	0.96[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs17742923	1.00[CHD][hapmap]
rs1808919	0.89[AMR][1000 genomes]
rs1838100	0.97[AMR][1000 genomes]
rs1838101	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1867235	0.92[AMR][1000 genomes]
rs2083790	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2218350	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2363753	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4246431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4968826	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4968962	0.92[AMR][1000 genomes]
rs4968967	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6501766	0.92[AMR][1000 genomes]
rs6501767	0.92[AMR][1000 genomes]
rs6501768	0.92[AMR][1000 genomes]
rs6501813	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6501835	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7209220	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7210022	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7211979	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]
rs7216817	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8068204	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]
rs8074944	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8082619	0.97[AMR][1000 genomes]
rs894593	0.92[AMR][1000 genomes]
rs894594	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980423	0.97[AMR][1000 genomes]
rs9895868	0.92[AMR][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	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	esv3377863	chr17:66883257-66885205	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6501839	ABCA9	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr17:66877000-66883800	Strong transcription	Adipose Nuclei	Adipose
3	chr17:66877000-66884000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr17:66877000-66886200	Weak transcription	Colonic Mucosa	Colon
5	chr17:66877000-66886600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr17:66877000-66889000	Weak transcription	Spleen	Spleen
7	chr17:66877000-66906200	Weak transcription	Fetal Stomach	stomach
8	chr17:66877200-66887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr17:66877600-66888400	Strong transcription	Liver	Liver
10	chr17:66877600-66893400	Weak transcription	Brain Anterior Caudate	brain
11	chr17:66877800-66918200	Weak transcription	Fetal Brain Male	brain
12	chr17:66878200-66889400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:66878200-66899200	Weak transcription	Osteobl	bone
14	chr17:66878400-66901000	Weak transcription	Brain Angular Gyrus	brain
15	chr17:66879800-66892600	Weak transcription	Fetal Muscle Leg	muscle
16	chr17:66879800-66897000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr17:66880000-66893400	Weak transcription	Brain Hippocampus Middle	brain
18	chr17:66880800-66883800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:66881000-66903200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr17:66881200-66893400	Weak transcription	Brain Substantia Nigra	brain
21	chr17:66881200-66904200	Weak transcription	Psoas Muscle	Psoas
22	chr17:66881400-66892800	Weak transcription	Fetal Heart	heart
23	chr17:66881400-66893600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:66881400-66893800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:66881400-66898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:66881400-66906400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr17:66881400-66906400	Weak transcription	Right Ventricle	heart
28	chr17:66881600-66893000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr17:66882000-66897600	Weak transcription	Left Ventricle	heart
30	chr17:66882400-66883800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:66882800-66890800	Strong transcription	Fetal Lung	lung
32	chr17:66883200-66884000	Strong transcription	Ovary	ovary
33	chr17:66883400-66890200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:66883400-66891800	Weak transcription	Aorta	Aorta
35	chr17:66883600-66885800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links