Variant report

Variant	rs12206905
Chromosome Location	chr6:38467664-38467665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38466684..38468343-chr6:38470238..38473899,3	MCF-7	breast:
2	chr6:38461115..38463494-chr6:38466391..38469115,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1033480	1.00[CHB][hapmap]
rs1205108	1.00[CHB][hapmap]
rs1883610	0.86[JPT][hapmap]
rs1983605	1.00[JPT][hapmap]
rs228179	1.00[CHB][hapmap]
rs228186	1.00[CHB][hapmap]
rs228188	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4236058	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4711542	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4711546	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4714152	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4714157	1.00[JPT][hapmap]
rs4714164	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4714165	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs6899746	1.00[JPT][hapmap]
rs6901086	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6904723	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6933268	1.00[JPT][hapmap]
rs6933758	1.00[JPT][hapmap]
rs6940319	1.00[JPT][hapmap]
rs742515	1.00[JPT][hapmap]
rs7748599	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7749685	1.00[JPT][hapmap]
rs7759629	1.00[JPT][hapmap]
rs7763775	1.00[CHB][hapmap]
rs7766214	1.00[JPT][hapmap]
rs7770868	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs871183	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9349073	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9357272	1.00[JPT][hapmap]
rs9380743	1.00[JPT][hapmap]
rs9394495	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394500	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9470885	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9470888	1.00[JPT][hapmap]
rs9470891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12206905	NFYA	cis	cerebellum	SCAN
rs12206905	MDFI	cis	cerebellum	SCAN
rs12206905	ANKS1A	cis	cerebellum	SCAN
rs12206905	GLO1	cis	parietal	SCAN
rs12206905	GLO1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38450600-38469800	Weak transcription	HSMMtube	muscle
3	chr6:38451600-38471000	Weak transcription	Psoas Muscle	Psoas
4	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:38454400-38486400	Weak transcription	Primary T cells from cord blood	blood
6	chr6:38460800-38473000	Enhancers	Brain Germinal Matrix	brain
7	chr6:38461000-38467800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:38462200-38471200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:38462800-38468000	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:38464200-38468600	Enhancers	Fetal Brain Male	brain
11	chr6:38466200-38468600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:38466400-38468200	Enhancers	Fetal Brain Female	brain
13	chr6:38466600-38468600	Enhancers	Adipose Nuclei	Adipose
14	chr6:38467000-38468200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:38467200-38468000	Enhancers	Brain Hippocampus Middle	brain
16	chr6:38467200-38476400	Weak transcription	Ovary	ovary
17	chr6:38467400-38467800	Enhancers	Brain Angular Gyrus	brain
18	chr6:38467400-38467800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr6:38467400-38467800	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr6:38467400-38468000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:38467400-38468000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:38467400-38476400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:38467600-38467800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:38467600-38468000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:38467600-38469600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:38467600-38469800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:38467600-38470600	Weak transcription	Brain Inferior Temporal Lobe	brain

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