Variant report

Variant	rs16870093
Chromosome Location	chr8:104117091-104117092
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104116308..104117555-chr8:104219520..104220293,3	MCF-7	breast:
2	chr8:104110536..104112989-chr8:104114800..104117513,2	MCF-7	breast:
3	chr8:104116094..104117635-chr8:104276900..104277894,4	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10505036	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505037	0.93[ASN][1000 genomes]
rs1587275	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16870084	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16870087	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16870094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17201317	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs17201513	0.83[ASN][1000 genomes]
rs1982974	0.98[ASN][1000 genomes]
rs28445282	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28506485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28582919	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28763628	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62525330	0.83[ASN][1000 genomes]
rs62525331	0.83[ASN][1000 genomes]
rs62525335	0.98[ASN][1000 genomes]
rs62525336	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62527570	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6983249	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983904	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825005	0.97[ASN][1000 genomes]
rs871516	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs871517	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872585	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872586	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv891247	chr8:104090979-104121862	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16870093	COX6C	cis	cerebellum	SCAN
rs16870093	BAALC	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104092400-104121600	Weak transcription	Right Atrium	heart
2	chr8:104116000-104118600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:104116000-104119200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr8:104116200-104117400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:104116400-104118200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr8:104116600-104117200	Enhancers	Osteobl	bone
7	chr8:104116600-104117400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:104116600-104117400	Enhancers	Brain Cingulate Gyrus	brain
9	chr8:104116600-104117400	Enhancers	Brain Hippocampus Middle	brain
10	chr8:104116600-104118000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:104116600-104118000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:104116600-104118000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:104116600-104118200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr8:104116600-104118200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr8:104116600-104118600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:104116600-104118800	Enhancers	NHDF-Ad	bronchial
17	chr8:104116600-104119000	Enhancers	Brain Substantia Nigra	brain
18	chr8:104116800-104117200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:104116800-104117400	Enhancers	Brain Anterior Caudate	brain
20	chr8:104116800-104117600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:104116800-104117600	Flanking Active TSS	NH-A	brain
22	chr8:104116800-104117800	Enhancers	HSMM	muscle
23	chr8:104116800-104118000	Enhancers	HMEC	breast
24	chr8:104116800-104118600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr8:104116800-104118600	Enhancers	Brain Germinal Matrix	brain
26	chr8:104116800-104118600	Enhancers	Left Ventricle	heart
27	chr8:104116800-104119000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr8:104116800-104119000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr8:104116800-104119000	Enhancers	NHLF	lung
30	chr8:104116800-104119200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:104116800-104119600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:104116800-104119800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr8:104116800-104123400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr8:104116800-104124200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr8:104117000-104117200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr8:104117000-104117400	Enhancers	Colon Smooth Muscle	Colon
37	chr8:104117000-104117600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr8:104117000-104117600	Enhancers	Fetal Stomach	stomach
39	chr8:104117000-104117800	Enhancers	Adipose Nuclei	Adipose
40	chr8:104117000-104118000	Weak transcription	Fetal Brain Female	brain
41	chr8:104117000-104118200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:104117000-104118400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr8:104117000-104119000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr8:104117000-104119000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr8:104117000-104124200	Enhancers	Brain Angular Gyrus	brain

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