Variant report

Variant	rs9470891
Chromosome Location	chr6:38467509-38467510
allele	A/C
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: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1033480	1.00[CHB][hapmap]
rs1205108	1.00[CHB][hapmap]
rs12206905	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]
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]
rs4236058	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][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	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][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	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9462436	0.90[YRI][hapmap]
rs9470885	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9470888	1.00[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9470891	NFYA	cis	cerebellum	SCAN
rs9470891	ANKS1A	cis	cerebellum	SCAN
rs9470891	GLO1	cis	parietal	SCAN
rs9470891	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	chr6:38462800-38467600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:38462800-38468000	Enhancers	Brain Cingulate Gyrus	brain
11	chr6:38463200-38467600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:38464200-38468600	Enhancers	Fetal Brain Male	brain
13	chr6:38466200-38468600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:38466400-38468200	Enhancers	Fetal Brain Female	brain
15	chr6:38466600-38467600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:38466600-38467600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:38466600-38468600	Enhancers	Adipose Nuclei	Adipose
18	chr6:38467000-38468200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:38467200-38467600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr6:38467200-38468000	Enhancers	Brain Hippocampus Middle	brain
21	chr6:38467200-38476400	Weak transcription	Ovary	ovary
22	chr6:38467400-38467800	Enhancers	Brain Angular Gyrus	brain
23	chr6:38467400-38467800	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr6:38467400-38467800	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr6:38467400-38468000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:38467400-38468000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:38467400-38476400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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