Variant report

Variant	rs979670
Chromosome Location	chr8:104117387-104117388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104116308..104117555-chr8:104219520..104220293,3	MCF-7	breast:
2	chr8:104110536..104112989-chr8:104114800..104117513,2	MCF-7	breast:
3	chr8:104116094..104117635-chr8:104276900..104277894,4	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2388492	0.87[ASN][1000 genomes]
rs2454015	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2454018	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454021	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454023	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454025	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454026	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515172	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2515212	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019170	0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs979672	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv891247	chr8:104090979-104121862	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs979670	BAALC	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104092400-104121600	Weak transcription	Right Atrium	heart
2	chr8:104116000-104118600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:104116000-104119200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr8:104116200-104117400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:104116400-104118200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr8:104116600-104117400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:104116600-104117400	Enhancers	Brain Cingulate Gyrus	brain
8	chr8:104116600-104117400	Enhancers	Brain Hippocampus Middle	brain
9	chr8:104116600-104118000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:104116600-104118000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr8:104116600-104118000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:104116600-104118200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr8:104116600-104118200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr8:104116600-104118600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:104116600-104118800	Enhancers	NHDF-Ad	bronchial
16	chr8:104116600-104119000	Enhancers	Brain Substantia Nigra	brain
17	chr8:104116800-104117400	Enhancers	Brain Anterior Caudate	brain
18	chr8:104116800-104117600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:104116800-104117600	Flanking Active TSS	NH-A	brain
20	chr8:104116800-104117800	Enhancers	HSMM	muscle
21	chr8:104116800-104118000	Enhancers	HMEC	breast
22	chr8:104116800-104118600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr8:104116800-104118600	Enhancers	Brain Germinal Matrix	brain
24	chr8:104116800-104118600	Enhancers	Left Ventricle	heart
25	chr8:104116800-104119000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr8:104116800-104119000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr8:104116800-104119000	Enhancers	NHLF	lung
28	chr8:104116800-104119200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:104116800-104119600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:104116800-104119800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr8:104116800-104123400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr8:104116800-104124200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr8:104117000-104117400	Enhancers	Colon Smooth Muscle	Colon
34	chr8:104117000-104117600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:104117000-104117600	Enhancers	Fetal Stomach	stomach
36	chr8:104117000-104117800	Enhancers	Adipose Nuclei	Adipose
37	chr8:104117000-104118000	Weak transcription	Fetal Brain Female	brain
38	chr8:104117000-104118200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:104117000-104118400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr8:104117000-104119000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:104117000-104119000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr8:104117000-104124200	Enhancers	Brain Angular Gyrus	brain
43	chr8:104117200-104117400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr8:104117200-104117600	Enhancers	Fetal Muscle Leg	muscle
45	chr8:104117200-104117600	Enhancers	HSMMtube	muscle
46	chr8:104117200-104117600	Flanking Active TSS	Osteobl	bone
47	chr8:104117200-104117800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr8:104117200-104117800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr8:104117200-104117800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr8:104117200-104117800	Enhancers	NHEK	skin

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