Variant report

Variant	rs13259545
Chromosome Location	chr8:104163759-104163760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104162104..104164227-chr8:104176288..104178946,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10088491	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10113728	0.83[YRI][hapmap]
rs10955310	0.91[ASN][1000 genomes]
rs12056711	1.00[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]
rs12545903	0.98[ASN][1000 genomes]
rs13264626	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13274504	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1494276	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1497449	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1845430	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249256	0.83[JPT][hapmap]
rs2256164	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2454013	0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2454014	0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2515190	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2515191	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2935579	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs4734071	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4734689	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4734690	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61274078	0.99[ASN][1000 genomes]
rs7001897	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7014418	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72507596	0.99[ASN][1000 genomes]
rs72671377	0.98[ASN][1000 genomes]
rs991312	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	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	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
3	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13259545	FZD6	cis	cerebellum	SCAN
rs13259545	FZD6	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104154000-104177200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:104155600-104165400	Genic enhancers	Primary hematopoietic stem cells	blood
3	chr8:104156400-104164200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr8:104156400-104164200	Weak transcription	Osteobl	bone
5	chr8:104158200-104164600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:104159800-104166200	Enhancers	Brain Cingulate Gyrus	brain
7	chr8:104161600-104166200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr8:104162000-104165600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
9	chr8:104162000-104168000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:104162200-104164400	Enhancers	Brain Angular Gyrus	brain
11	chr8:104162400-104166200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:104162400-104169000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:104162600-104164000	Enhancers	Brain Hippocampus Middle	brain
14	chr8:104162600-104165600	Enhancers	Adipose Nuclei	Adipose
15	chr8:104162600-104166000	Enhancers	Left Ventricle	heart
16	chr8:104162600-104166800	Enhancers	Brain Substantia Nigra	brain
17	chr8:104162800-104164000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:104162800-104164000	Enhancers	Brain Anterior Caudate	brain
19	chr8:104162800-104164000	Weak transcription	Fetal Brain Male	brain
20	chr8:104162800-104165400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:104162800-104165600	Enhancers	Primary B cells from peripheral blood	blood
22	chr8:104162800-104166000	Enhancers	HUVEC	blood vessel
23	chr8:104162800-104166200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr8:104162800-104172600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr8:104163000-104164800	Enhancers	Fetal Muscle Leg	muscle
26	chr8:104163000-104165200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:104163000-104165600	Enhancers	Fetal Stomach	stomach
28	chr8:104163400-104163800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr8:104163400-104164000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:104163400-104165000	Enhancers	Right Atrium	heart
31	chr8:104163400-104165400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr8:104163400-104166200	Enhancers	Spleen	Spleen
33	chr8:104163600-104163800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr8:104163600-104163800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr8:104163600-104164000	Enhancers	Right Ventricle	heart
36	chr8:104163600-104164600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr8:104163600-104164600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:104163600-104164800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr8:104163600-104164800	Enhancers	Fetal Brain Female	brain
40	chr8:104163600-104165000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:104163600-104165000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr8:104163600-104165000	Enhancers	Lung	lung
43	chr8:104163600-104165200	Enhancers	Primary B cells from cord blood	blood
44	chr8:104163600-104166600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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