Variant report

Variant	rs6878665
Chromosome Location	chr5:108062630-108062631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:102455042..102457413-chr5:108061367..108063051,2	K562	blood:
2	chr5:108060235..108074407-chr5:108078172..108087811,48	K562	blood:
3	chr5:108062598..108065696-chr5:108743430..108747045,3	K562	blood:
4	chr5:108062273..108066431-chr5:108081834..108086243,5	MCF-7	breast:
5	chr5:108062575..108065883-chr5:108081229..108085721,5	MCF-7	breast:
6	chr5:108061248..108063366-chr5:108744728..108747196,2	MCF-7	breast:
7	chr5:108043545..108045265-chr5:108061960..108063883,2	K562	blood:
8	chr5:108061485..108063764-chr5:108531094..108533966,2	K562	blood:
9	chr5:108034866..108037044-chr5:108060697..108062781,2	K562	blood:
10	chr5:108059312..108068052-chr5:108079113..108087366,42	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FER-1	chr5:108061406-108063661	XLOC_004501
2	lnc-FBXL17-2	chr5:108061406-108063661	NONHSAT103127

No data

Variant related genes	Relation type
ENSG00000198961	Chromatin interaction
ENSG00000145725	Chromatin interaction
ENSG00000145723	Chromatin interaction
ENSG00000151422	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs57977516	0.86[AFR][1000 genomes]
rs60521409	0.85[AMR][1000 genomes]
rs6893743	0.94[LWK][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs73222008	0.85[AMR][1000 genomes]
rs73222009	0.85[AMR][1000 genomes]
rs73222017	0.82[AFR][1000 genomes]
rs73222021	0.85[AMR][1000 genomes]
rs73222022	0.85[AMR][1000 genomes]
rs73222025	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6878665	BCAT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108061800-108062800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr5:108062200-108062800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:108062200-108062800	Enhancers	Pancreas	Pancrea
4	chr5:108062200-108062800	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr5:108062200-108062800	Enhancers	HMEC	breast
6	chr5:108062200-108063000	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:108062200-108063000	Enhancers	Esophagus	oesophagus
8	chr5:108062200-108063000	Enhancers	Fetal Brain Female	brain
9	chr5:108062200-108063000	Enhancers	Dnd41	blood
10	chr5:108062200-108063400	Enhancers	Spleen	Spleen
11	chr5:108062200-108063400	Flanking Active TSS	GM12878-XiMat	blood
12	chr5:108062200-108064000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:108062200-108065000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:108062400-108062800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:108062400-108062800	Weak transcription	Aorta	Aorta
16	chr5:108062400-108062800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:108062400-108062800	Enhancers	Stomach Mucosa	stomach
18	chr5:108062400-108062800	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr5:108062400-108063000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr5:108062400-108063000	Enhancers	Primary B cells from cord blood	blood
21	chr5:108062400-108063000	Enhancers	Brain Substantia Nigra	brain
22	chr5:108062400-108063000	Enhancers	HUVEC	blood vessel
23	chr5:108062400-108063200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:108062400-108063400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr5:108062400-108063400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:108062400-108065000	Active TSS	Brain Hippocampus Middle	brain
27	chr5:108062600-108062800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr5:108062600-108062800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:108062600-108062800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:108062600-108062800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr5:108062600-108062800	Flanking Active TSS	Fetal Kidney	kidney
32	chr5:108062600-108062800	Enhancers	Rectal Smooth Muscle	rectum
33	chr5:108062600-108062800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:108062600-108062800	Flanking Active TSS	A549	lung
35	chr5:108062600-108062800	Transcr. at gene 5' and 3'	K562	blood
36	chr5:108062600-108063000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:108062600-108063000	Enhancers	Primary hematopoietic stem cells	blood
38	chr5:108062600-108063000	Enhancers	Brain Angular Gyrus	brain
39	chr5:108062600-108063000	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr5:108062600-108063000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr5:108062600-108063200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr5:108062600-108063200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:108062600-108063200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:108062600-108063200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:108062600-108063200	Enhancers	Placenta	Placenta
46	chr5:108062600-108063400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr5:108062600-108063400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr5:108062600-108063400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr5:108062600-108063400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:108062600-108063400	Flanking Active TSS	NHDF-Ad	bronchial

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