Variant report

Variant	rs7840976
Chromosome Location	chr8:104134123-104134124
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	chr8:104131678..104134497-chr8:104225293..104227549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164929	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs60670387	0.95[AFR][1000 genomes]
rs62527572	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62527573	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62527574	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62527608	0.83[EUR][1000 genomes]
rs62527610	0.83[EUR][1000 genomes]
rs62527613	0.83[EUR][1000 genomes]
rs7006682	0.83[EUR][1000 genomes]
rs73701726	0.95[AFR][1000 genomes]
rs73701728	0.95[AFR][1000 genomes]
rs73701729	0.95[AFR][1000 genomes]
rs73701731	0.95[AFR][1000 genomes]
rs73701732	0.95[AFR][1000 genomes]
rs73701734	0.95[AFR][1000 genomes]
rs73701735	0.95[AFR][1000 genomes]
rs73701736	0.87[AFR][1000 genomes]
rs73701737	0.91[AFR][1000 genomes]
rs73701738	0.95[AFR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7840976	BAALC	cis	cerebellum	SCAN
rs7840976	DCAF13	cis	cerebellum	SCAN
rs7840976	C8orf56	cis	cerebellum	SCAN
rs7840976	BAALC	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104122000-104134600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:104128800-104134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:104131000-104135200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:104131200-104136400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:104132000-104134400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:104132200-104134200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:104132200-104135600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr8:104132200-104139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:104132400-104134600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr8:104132400-104134600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr8:104132400-104134600	Weak transcription	HUVEC	blood vessel
12	chr8:104132400-104135400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:104132600-104134400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:104132600-104134600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:104132600-104135200	Weak transcription	GM12878-XiMat	blood
16	chr8:104132600-104135200	Weak transcription	NH-A	brain
17	chr8:104132600-104135800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr8:104132800-104134200	Enhancers	NHEK	skin
19	chr8:104132800-104134600	Weak transcription	Lung	lung
20	chr8:104132800-104134800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr8:104132800-104137000	Weak transcription	Brain Substantia Nigra	brain
22	chr8:104132800-104137200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:104133000-104134200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:104133000-104137000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr8:104133200-104134200	Enhancers	HSMMtube	muscle
26	chr8:104133200-104137000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr8:104133200-104137000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr8:104133200-104137200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr8:104133200-104137400	Weak transcription	Brain Angular Gyrus	brain
30	chr8:104133400-104134600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr8:104133400-104135000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:104133400-104135800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr8:104133400-104135800	Enhancers	Osteobl	bone
34	chr8:104133400-104137000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr8:104133400-104137200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr8:104133600-104134400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr8:104133600-104135000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr8:104133600-104135400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr8:104133600-104135600	Enhancers	NHDF-Ad	bronchial
40	chr8:104133800-104134800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr8:104133800-104135600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr8:104134000-104134200	Enhancers	Brain Anterior Caudate	brain
43	chr8:104134000-104134200	Enhancers	Fetal Intestine Large	intestine
44	chr8:104134000-104135000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr8:104134000-104135200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr8:104134000-104135600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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