Variant report

Variant	rs11077859
Chromosome Location	chr17:66971879-66971880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11077884	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11453	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.99[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];0.88[TSI][hapmap];0.80[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	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12940103	0.82[EUR][1000 genomes]
rs12942599	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12943969	0.82[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];0.99[ASN][1000 genomes]
rs16973495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191212	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191213	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302291	1.00[YRI][hapmap]
rs2302292	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302293	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302294	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]
rs36096265	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4548939	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968983	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.98[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];0.89[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];0.89[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];0.93[ASN][1000 genomes]
rs8070285	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs8070357	0.88[ASN][1000 genomes]
rs9894490	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	nsv908703	chr17:66904001-66978319	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv3506425	chr17:66971559-66973166	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	n/a
9	esv3506426	chr17:66971559-66973166	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11077859	ABCA6	cis	parietal	SCAN
rs11077859	C17orf58	cis	cerebellum	SCAN
rs11077859	TACO1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66965600-66973200	Weak transcription	Brain Substantia Nigra	brain
2	chr17:66965600-66977600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr17:66965600-66980200	Weak transcription	Brain Anterior Caudate	brain
4	chr17:66965600-66986000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:66966200-66977200	Weak transcription	Fetal Muscle Leg	muscle
6	chr17:66966800-66972000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:66968400-66972600	Weak transcription	Fetal Lung	lung
8	chr17:66968400-66977200	Weak transcription	NHDF-Ad	bronchial
9	chr17:66969200-66982800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr17:66969400-66972400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr17:66969600-66977200	Weak transcription	HepG2	liver
12	chr17:66970000-66973600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:66970200-66974200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:66970400-66972400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:66970800-66984000	Weak transcription	Spleen	Spleen
16	chr17:66971000-66987800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:66971200-66974000	Strong transcription	Adipose Nuclei	Adipose
18	chr17:66971200-66974000	Strong transcription	Liver	Liver
19	chr17:66971200-66974000	Strong transcription	Ovary	ovary
20	chr17:66971200-66974000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr17:66971800-66972400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr17:66971800-66974000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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