Variant report

Variant	rs7001084
Chromosome Location	chr8:104226946-104226947
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	chr8:104226501..104229648-chr8:104233395..104236650,3	MCF-7	breast:
2	chr8:104131678..104134497-chr8:104225293..104227549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250929	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10096928	0.84[ASN][1000 genomes]
rs1157213	0.90[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs13270175	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13277869	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs1494280	0.81[ASN][1000 genomes]
rs17205332	0.80[CHB][hapmap]
rs2220824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3104033	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs3133833	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3133837	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs4510824	0.88[ASN][1000 genomes]
rs4734692	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6999018	0.82[ASN][1000 genomes]
rs7015757	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7825986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7829782	0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[ASN][1000 genomes]
rs9656787	0.82[JPT][hapmap]

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	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
5	esv14660	chr8:104182119-104245529	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7001084	NACAP1	cis	parietal	SCAN
rs7001084	SLC25A32	cis	cerebellum	SCAN
rs7001084	BAALC	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104220400-104229400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr8:104222400-104240800	Weak transcription	Gastric	stomach
3	chr8:104222400-104241200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr8:104222600-104227600	Weak transcription	Osteobl	bone
5	chr8:104222800-104227200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr8:104222800-104240800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:104222800-104241000	Weak transcription	NHDF-Ad	bronchial
8	chr8:104223600-104228000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr8:104223600-104231600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:104224000-104227400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr8:104224200-104228200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:104224600-104227000	Weak transcription	Fetal Brain Female	brain
13	chr8:104224800-104228200	Strong transcription	Brain Hippocampus Middle	brain
14	chr8:104225200-104227400	Strong transcription	Brain Anterior Caudate	brain
15	chr8:104225200-104228000	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr8:104225400-104228000	Strong transcription	Brain Cingulate Gyrus	brain
17	chr8:104225400-104240400	Weak transcription	Brain Angular Gyrus	brain
18	chr8:104225600-104227000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:104225600-104227400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr8:104225600-104233000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:104225800-104227000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:104225800-104227800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:104225800-104229800	Weak transcription	Fetal Stomach	stomach
24	chr8:104226200-104228000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr8:104226400-104227000	Weak transcription	Brain Substantia Nigra	brain
26	chr8:104226400-104242800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:104226600-104234800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr8:104226800-104227600	Strong transcription	Fetal Brain Male	brain
29	chr8:104226800-104232400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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