Variant report

Variant	rs2439592
Chromosome Location	chr5:112070122-112070123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr5:112070026-112070704	K562	blood:	n/a	n/a
2	ARID3A	chr5:112069769-112070489	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112041577..112049243-chr5:112069735..112074802,8	K562	blood:
2	chr5:112030715..112032884-chr5:112068786..112071232,2	K562	blood:
3	chr5:112063462..112066944-chr5:112067899..112070429,3	K562	blood:
4	chr5:112060614..112062954-chr5:112069496..112072415,2	K562	blood:
5	chr5:111496324..111497979-chr5:112068139..112070715,2	K562	blood:
6	chr5:112041486..112046402-chr5:112068342..112076365,12	K562	blood:
7	chr5:112065585..112071178-chr5:112071889..112074120,7	K562	blood:
8	chr5:112068435..112070448-chr5:112071889..112074072,3	K562	blood:

No data

Variant related genes	Relation type
APC	TF binding region
ENSG00000238363	Chromatin interaction
ENSG00000134982	Chromatin interaction
ENSG00000224032	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11953943	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11960216	0.97[EUR][1000 genomes]
rs1644241	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1644242	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1661032	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1661034	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1697914	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1697916	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17134960	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs1734244	0.92[EUR][1000 genomes]
rs1734245	0.90[CEU][hapmap]
rs1734246	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1734247	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1882619	1.00[GIH][hapmap];0.82[AMR][1000 genomes]
rs2229994	1.00[YRI][hapmap]
rs2431505	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2431507	0.90[CEU][hapmap];0.95[GIH][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2431508	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2431509	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2431511	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2439590	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2439593	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2439594	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2455294	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2455296	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2464802	0.84[EUR][1000 genomes]
rs2464808	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2464810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2909784	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2909961	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2909962	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs73220022	0.84[EUR][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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
2	chr5:112052000-112072600	Weak transcription	Primary B cells from cord blood	blood
3	chr5:112052600-112072600	Weak transcription	Primary T cells from cord blood	blood
4	chr5:112054400-112073200	Weak transcription	Pancreas	Pancrea
5	chr5:112058600-112072800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:112059200-112073200	Weak transcription	Left Ventricle	heart
7	chr5:112060000-112072800	Weak transcription	Fetal Heart	heart
8	chr5:112061000-112072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:112061000-112072800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:112061000-112073000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:112061800-112073000	Weak transcription	Fetal Stomach	stomach
12	chr5:112062200-112073000	Weak transcription	Brain Germinal Matrix	brain
13	chr5:112062400-112072800	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:112062400-112073000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:112062400-112073000	Weak transcription	Fetal Intestine Small	intestine
16	chr5:112065200-112073000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:112065400-112070800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:112066000-112070800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:112066400-112072800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:112066400-112072800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:112067000-112072800	Weak transcription	Fetal Kidney	kidney
22	chr5:112067400-112071400	Weak transcription	Brain Anterior Caudate	brain
23	chr5:112067800-112071600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:112067800-112073000	Weak transcription	Psoas Muscle	Psoas
25	chr5:112068000-112070600	Weak transcription	HSMMtube	muscle
26	chr5:112068000-112072200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:112068200-112073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:112068400-112070800	Weak transcription	HUVEC	blood vessel
29	chr5:112068600-112072600	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:112069000-112072800	Enhancers	K562	blood
31	chr5:112069000-112072800	Enhancers	NHDF-Ad	bronchial
32	chr5:112069200-112071000	Enhancers	Brain Substantia Nigra	brain
33	chr5:112069200-112072800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:112069200-112073000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:112069200-112073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:112069400-112071600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:112069600-112070200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:112069600-112071000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:112069600-112071400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:112069600-112073000	Weak transcription	HMEC	breast
41	chr5:112069800-112070600	Weak transcription	Osteobl	bone
42	chr5:112069800-112070800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:112069800-112071400	Weak transcription	Hela-S3	cervix
44	chr5:112069800-112072400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:112069800-112072800	Weak transcription	NHEK	skin
46	chr5:112069800-112073000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:112070000-112070600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:112070000-112070800	Enhancers	Brain Hippocampus Middle	brain
49	chr5:112070000-112071400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:112070000-112072800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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