Variant report

Variant	rs2302294
Chromosome Location	chr17:66985992-66985993
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10512523	0.90[CHB][hapmap]
rs11077858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077884	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11453	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11657541	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11871766	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs11871944	1.00[ASW][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12325889	0.90[CHB][hapmap]
rs12939564	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12940103	0.81[EUR][1000 genomes]
rs12942599	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12943969	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1541470	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16973495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191212	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191213	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302291	1.00[YRI][hapmap]
rs2302292	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302293	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36096265	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4548939	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968983	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6501944	0.86[JPT][hapmap]
rs6501947	0.89[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs7207125	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7215642	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs7217543	0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs7218871	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8066758	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8068236	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8070285	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs8070357	0.90[ASN][1000 genomes]
rs9894490	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2302294	ABCA9	cis	parietal	SCAN
rs2302294	TACO1	cis	cerebellum	SCAN
rs2302294	C17orf58	cis	cerebellum	SCAN
rs2302294	ABCA6	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66965600-66986000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:66971000-66987800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr17:66977400-66989400	Weak transcription	Pancreas	Pancrea
4	chr17:66977600-67001400	Weak transcription	Fetal Lung	lung
5	chr17:66977800-66987600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:66977800-66991000	Weak transcription	Fetal Stomach	stomach
7	chr17:66977800-66991600	Strong transcription	Adipose Nuclei	Adipose
8	chr17:66977800-67027400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr17:66978600-66987200	Weak transcription	NHDF-Ad	bronchial
10	chr17:66978600-66988000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:66978600-66989400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:66979400-67005400	Weak transcription	Psoas Muscle	Psoas
13	chr17:66979600-67001200	Weak transcription	Left Ventricle	heart
14	chr17:66980400-67009400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr17:66981400-67001200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr17:66981400-67001400	Weak transcription	Fetal Muscle Leg	muscle
17	chr17:66982600-66990000	Strong transcription	Liver	Liver
18	chr17:66983600-66988000	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:66985000-66986400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:66985400-66988200	Strong transcription	Ovary	ovary
21	chr17:66985600-66986000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr17:66985600-66986400	Enhancers	Brain Substantia Nigra	brain
23	chr17:66985600-66988000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr17:66985800-66986200	Enhancers	Brain Hippocampus Middle	brain

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