Variant report

Variant	rs6883028
Chromosome Location	chr5:52290094-52290095
allele	A/T
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:5)
LncRNA
region (count:1)
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	POLR2A	chr5:52290023-52290474	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr5:52289897-52290563	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:52287570..52290507-chr5:52297245..52299058,2	MCF-7	breast:
2	chr5:52284537..52287438-chr5:52289001..52291401,4	MCF-7	breast:
3	chr5:52287901..52290762-chr5:52300870..52303377,2	MCF-7	breast:
4	chr5:52288695..52291271-chr5:52292952..52294743,2	MCF-7	breast:
5	chr5:52285332..52287022-chr5:52289921..52292396,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA1-1	chr5:52286944-52290794	ucscGeneNc_uc003jox_1

No data

Variant related genes	Relation type
ENSG00000249899	TF binding region
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10042752	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10058636	0.91[ASN][1000 genomes]
rs10061730	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10065796	1.00[JPT][hapmap]
rs10071255	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10071580	0.97[ASN][1000 genomes]
rs10073544	1.00[JPT][hapmap]
rs11948978	0.97[ASN][1000 genomes]
rs12523395	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1363188	0.80[CEU][hapmap]
rs1421941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16880539	0.89[CEU][hapmap]
rs16880541	0.80[CEU][hapmap]
rs16880636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1862639	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3212386	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs3212402	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3212412	0.97[ASN][1000 genomes]
rs3212417	0.97[ASN][1000 genomes]
rs3212627	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs55783963	0.97[ASN][1000 genomes]
rs67217308	0.97[ASN][1000 genomes]
rs67835512	0.97[ASN][1000 genomes]
rs9292002	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9292003	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][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	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 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	chr5:52286200-52295400	Weak transcription	Pancreas	Pancrea
2	chr5:52286200-52300400	Weak transcription	Gastric	stomach
3	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
4	chr5:52286200-52313600	Weak transcription	Lung	lung
5	chr5:52286600-52291000	Weak transcription	Esophagus	oesophagus
6	chr5:52286600-52292000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:52286600-52292600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:52286600-52293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
11	chr5:52286800-52290400	Transcr. at gene 5' and 3'	NHEK	skin
12	chr5:52286800-52294400	Weak transcription	Osteobl	bone
13	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
14	chr5:52287000-52291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:52287000-52292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:52287000-52293000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:52287000-52293400	Weak transcription	Fetal Intestine Small	intestine
18	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:52287200-52292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:52287200-52293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:52287200-52293400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:52287200-52293600	Weak transcription	Fetal Kidney	kidney
23	chr5:52287600-52290800	Transcr. at gene 5' and 3'	HMEC	breast
24	chr5:52288000-52292400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
25	chr5:52288200-52290200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:52288200-52290400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:52288800-52290800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:52288800-52290800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:52288800-52292000	Enhancers	NHDF-Ad	bronchial
30	chr5:52289000-52290800	Enhancers	Brain Substantia Nigra	brain
31	chr5:52289000-52291600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
32	chr5:52289200-52291000	Weak transcription	A549	lung
33	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:52289400-52290800	Enhancers	HUVEC	blood vessel
35	chr5:52289400-52292000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:52289400-52295600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:52289600-52290200	Weak transcription	Hela-S3	cervix
38	chr5:52289600-52290600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:52289600-52290800	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:52289600-52291000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:52289800-52290600	Genic enhancers	HepG2	liver
42	chr5:52290000-52290600	Enhancers	NHLF	lung
43	chr5:52290000-52290800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:52290000-52292800	Enhancers	Brain Anterior Caudate	brain
45	chr5:52290000-52299800	Weak transcription	NH-A	brain

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