Variant report

Variant	rs62279954
Chromosome Location	chr3:161134554-161134555
allele	A/C
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:0)
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	chr3:160786404..160789728-chr3:161132273..161134989,3	MCF-7	breast:
2	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
3	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
4	chr17:59472839..59476239-chr3:161133074..161135554,3	MCF-7	breast:
5	chr3:161040559..161042979-chr3:161133154..161135842,2	MCF-7	breast:
6	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
7	chr3:160938218..160944428-chr3:161134456..161142008,22	MCF-7	breast:
8	chr3:160817396..160819299-chr3:161134159..161136012,2	MCF-7	breast:
9	chr3:161134333..161136577-chr3:161138174..161140104,2	K562	blood:
10	chr3:160677412..160680256-chr3:161134462..161137137,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs16832063	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16832129	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16847274	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2035498	0.89[AMR][1000 genomes]
rs56839556	0.94[EUR][1000 genomes]
rs62279886	0.84[AMR][1000 genomes]
rs62279918	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279920	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279922	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279923	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279924	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279925	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279927	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279929	0.89[AMR][1000 genomes]
rs62279930	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62279931	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62279948	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62279949	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62279950	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62279955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73162552	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73162554	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73162598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:161129600-161134600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:161130600-161134800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:161131600-161140000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:161132400-161134600	Enhancers	Stomach Mucosa	stomach
6	chr3:161132800-161134600	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:161132800-161134600	Enhancers	NHDF-Ad	bronchial
8	chr3:161133000-161134600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:161133200-161134600	Enhancers	Liver	Liver
10	chr3:161133200-161134600	Enhancers	HMEC	breast
11	chr3:161133200-161134600	Enhancers	NHEK	skin
12	chr3:161133400-161134600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:161133400-161134600	Flanking Active TSS	A549	lung
14	chr3:161133600-161134600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:161133600-161134600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:161133800-161134800	Enhancers	Fetal Muscle Leg	muscle
17	chr3:161134000-161134600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:161134000-161134600	Enhancers	Aorta	Aorta
19	chr3:161134000-161134600	Enhancers	Esophagus	oesophagus
20	chr3:161134000-161134600	Enhancers	Pancreas	Pancrea
21	chr3:161134000-161138400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:161134200-161134600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:161134200-161134600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:161134200-161134600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:161134200-161134600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:161134200-161134600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:161134200-161134600	Flanking Active TSS	Hela-S3	cervix
28	chr3:161134200-161134600	Enhancers	NHLF	lung
29	chr3:161134200-161137400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:161134400-161134600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:161134400-161134600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:161134400-161134600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:161134400-161134600	Weak transcription	Left Ventricle	heart
34	chr3:161134400-161134600	Enhancers	HUVEC	blood vessel
35	chr3:161134400-161134600	Enhancers	NH-A	brain
36	chr3:161134400-161134600	Enhancers	Osteobl	bone
37	chr3:161134400-161137200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:161134400-161137400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:161134400-161137400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:161134400-161138400	Weak transcription	Fetal Lung	lung
41	chr3:161134400-161138600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:161134400-161139800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:161134400-161141200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:161134400-161145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:161134400-161148200	Weak transcription	Brain Inferior Temporal Lobe	brain

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