Variant report

Variant	rs1060242
Chromosome Location	chr8:67380528-67380529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57920618..57922939-chr8:67379137..67382122,2	MCF-7	breast:
2	chr8:67378228..67380679-chr8:67388244..67390416,2	MCF-7	breast:
3	chr8:67379259..67381817-chr8:67625879..67628203,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1025228	0.86[GIH][hapmap]
rs1030421	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs1108	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs13682	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs1426907	0.85[EUR][1000 genomes]
rs2059640	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059641	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357893	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357894	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465982	0.81[EUR][1000 genomes]
rs2465985	0.82[GIH][hapmap]
rs2465990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555568	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2555569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555570	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555571	0.87[EUR][1000 genomes]
rs2555572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555574	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555575	0.87[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2555587	0.86[EUR][1000 genomes]
rs2718988	0.87[GIH][hapmap]
rs2719000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2719002	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2719004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2719005	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2719006	0.87[EUR][1000 genomes]
rs2719008	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35352031	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4532579	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55878528	0.94[ASN][1000 genomes]
rs7014980	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs890515	0.87[EUR][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	esv3446467	chr8:66749863-67667068	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3414665	chr8:66936816-67381935	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv6236	chr8:67359312-67403981	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv465702	chr8:67375519-67385088	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv611457	chr8:67375519-67385088	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1026137	chr8:67376420-67408122	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1060242	C8orf46	cis	Adipose Subcutaneous	GTEx
rs1060242	C8orf46	cis	Artery Aorta	GTEx
rs1060242	ADHFE1	cis	Esophagus Muscularis	GTEx
rs1060242	ADHFE1	cis	cerebellum	SCAN
rs1060242	ADHFE1	cis	multi-tissue	Pritchard
rs1060242	C8orf46	cis	lung	GTEx
rs1060242	ADHFE1	cis	Thyroid	GTEx
rs1060242	ADHFE1	cis	Nerve Tibial	GTEx
rs1060242	C8orf46	cis	Nerve Tibial	GTEx
rs1060242	MYBL1	cis	parietal	SCAN
rs1060242	C8orf46	cis	Artery Tibial	GTEx
rs1060242	ADHFE1	cis	parietal	SCAN
rs1060242	ADHFE1	cis	Artery Tibial	GTEx
rs1060242	C8orf46	cis	Skin Sun Exposed Lower leg	GTEx
rs1060242	ADHFE1	cis	Heart Left Ventricle	GTEx
rs1060242	C8orf46	cis	Thyroid	GTEx
rs1060242	C8orf46	cis	multi-tissue	Pritchard
rs1060242	C8orf46	cis	Esophagus Mucosa	GTEx
rs1060242	ADHFE1	cis	Muscle Skeletal	GTEx
rs1060242	C8orf46	cis	Esophagus Muscularis	GTEx
rs1060242	C8orf46	cis	Stomach	GTEx
rs1060242	ADHFE1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:67359400-67384400	Weak transcription	Fetal Kidney	kidney
2	chr8:67364800-67384000	Weak transcription	Colon Smooth Muscle	Colon
3	chr8:67365400-67383800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:67368400-67384400	Weak transcription	Psoas Muscle	Psoas
5	chr8:67370800-67384200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:67371200-67383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:67371400-67384200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr8:67372600-67381000	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:67372600-67383600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:67372800-67381400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:67372800-67383600	Weak transcription	Brain Hippocampus Middle	brain
12	chr8:67372800-67384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:67372800-67395200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr8:67373000-67384400	Weak transcription	Brain Angular Gyrus	brain
15	chr8:67373800-67385400	Weak transcription	Fetal Intestine Small	intestine
16	chr8:67374000-67381200	Weak transcription	Spleen	Spleen
17	chr8:67374400-67382200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:67374800-67384600	Weak transcription	Lung	lung
19	chr8:67374800-67396800	Weak transcription	Pancreas	Pancrea
20	chr8:67375000-67384600	Weak transcription	Right Ventricle	heart
21	chr8:67376400-67382200	Weak transcription	NHEK	skin
22	chr8:67376400-67382800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:67376400-67383000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:67376400-67383800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr8:67376400-67384200	Weak transcription	HSMM	muscle
26	chr8:67376400-67390000	Weak transcription	Fetal Heart	heart
27	chr8:67376800-67380600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr8:67376800-67382200	Weak transcription	NH-A	brain
29	chr8:67376800-67383600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr8:67376800-67384000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:67376800-67384800	Weak transcription	Fetal Lung	lung
32	chr8:67377200-67381400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr8:67377200-67382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr8:67377200-67389400	Weak transcription	Brain Substantia Nigra	brain
35	chr8:67377400-67382800	Weak transcription	Hela-S3	cervix
36	chr8:67378200-67381800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr8:67378800-67380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr8:67378800-67380800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr8:67378800-67381000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr8:67378800-67381800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr8:67378800-67381800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr8:67379000-67381000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr8:67379000-67381000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr8:67379000-67381000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr8:67379200-67380800	Strong transcription	Brain Anterior Caudate	brain
46	chr8:67379200-67381000	Strong transcription	Placenta	Placenta
47	chr8:67379200-67381200	Enhancers	Liver	Liver
48	chr8:67379400-67380800	Strong transcription	Aorta	Aorta
49	chr8:67379400-67381000	Strong transcription	Adipose Nuclei	Adipose
50	chr8:67379400-67381600	Strong transcription	Ovary	ovary

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