Variant report

Variant	rs13143520
Chromosome Location	chr4:87842078-87842079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87840562..87842094-chr4:87856459..87858099,2	MCF-7	breast:
2	chr4:87841127..87845186-chr4:87926504..87931446,8	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029698	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10034541	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1075989	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12186239	0.90[EUR][1000 genomes]
rs13103212	0.86[EUR][1000 genomes]
rs13112444	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13114907	0.81[EUR][1000 genomes]
rs13117826	0.86[EUR][1000 genomes]
rs13131035	0.90[EUR][1000 genomes]
rs13131194	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13134746	0.86[EUR][1000 genomes]
rs13147942	0.86[EUR][1000 genomes]
rs13151671	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13151797	0.87[EUR][1000 genomes]
rs13434404	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2705623	0.86[EUR][1000 genomes]
rs28407685	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28439108	0.86[EUR][1000 genomes]
rs28447475	0.86[EUR][1000 genomes]
rs28457189	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28458234	0.99[EUR][1000 genomes]
rs28502831	0.90[EUR][1000 genomes]
rs28594717	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28610346	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28620528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28629974	0.90[EUR][1000 genomes]
rs28661703	0.89[EUR][1000 genomes]
rs28664715	0.90[EUR][1000 genomes]
rs28706796	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28729679	0.86[EUR][1000 genomes]
rs28854225	0.90[EUR][1000 genomes]
rs28886889	0.90[EUR][1000 genomes]
rs34077745	0.90[AMR][1000 genomes]
rs34991149	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35480728	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35667731	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36053558	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71605624	0.84[EUR][1000 genomes]
rs71605686	0.86[EUR][1000 genomes]
rs71605687	0.86[EUR][1000 genomes]
rs71605688	0.90[EUR][1000 genomes]
rs71605691	0.93[EUR][1000 genomes]
rs71605693	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7683045	0.86[EUR][1000 genomes]
rs7691435	1.00[ASN][1000 genomes]
rs9993812	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9999001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv980228	chr4:87834452-87845024	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87825600-87846000	Weak transcription	Gastric	stomach
2	chr4:87825600-87849400	Weak transcription	Lung	lung
3	chr4:87825600-87849400	Weak transcription	Spleen	Spleen
4	chr4:87825800-87843600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:87825800-87854800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:87825800-87854800	Weak transcription	Right Ventricle	heart
7	chr4:87825800-87855200	Weak transcription	Fetal Stomach	stomach
8	chr4:87826000-87852400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:87826200-87843000	Weak transcription	Liver	Liver
10	chr4:87826200-87843400	Weak transcription	Brain Substantia Nigra	brain
11	chr4:87829800-87855000	Weak transcription	Aorta	Aorta
12	chr4:87830200-87849600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:87830200-87855200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:87830400-87847600	Weak transcription	Thymus	Thymus
15	chr4:87830400-87847800	Weak transcription	Psoas Muscle	Psoas
16	chr4:87830400-87849400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:87830400-87854600	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:87830600-87843000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:87830600-87843400	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:87830600-87843400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:87830600-87845600	Weak transcription	Left Ventricle	heart
22	chr4:87831000-87855000	Weak transcription	Fetal Lung	lung
23	chr4:87831400-87854400	Weak transcription	Fetal Heart	heart
24	chr4:87831400-87854800	Weak transcription	Right Atrium	heart
25	chr4:87832200-87854800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:87835200-87849000	Weak transcription	Pancreas	Pancrea
27	chr4:87837200-87854400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:87838400-87843800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:87838400-87855000	Weak transcription	Colonic Mucosa	Colon
30	chr4:87838600-87844000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr4:87838800-87843000	Weak transcription	Hela-S3	cervix
32	chr4:87838800-87844000	Enhancers	NHDF-Ad	bronchial
33	chr4:87839000-87850200	Enhancers	Placenta	Placenta
34	chr4:87839600-87843800	Weak transcription	Fetal Intestine Small	intestine
35	chr4:87839600-87844000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:87839600-87844000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:87839600-87844200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:87839600-87847600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:87839800-87842800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:87840000-87843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:87840000-87844000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:87840000-87844000	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr4:87840200-87842400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:87840200-87843400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:87840200-87852200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:87840200-87854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:87840400-87843400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr4:87840400-87845800	Weak transcription	NHLF	lung
49	chr4:87840400-87847800	Weak transcription	HSMMtube	muscle
50	chr4:87840400-87849000	Weak transcription	GM12878-XiMat	blood

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