Variant report

Variant	rs27504
Chromosome Location	chr5:52288173-52288174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:52287981-52288241	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52287570..52290507-chr5:52297245..52299058,2	MCF-7	breast:
2	chr5:52287901..52290762-chr5:52300870..52303377,2	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000249899	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs152089	0.83[YRI][hapmap]
rs1541689	0.85[YRI][hapmap]
rs1904165	0.82[CHB][hapmap]
rs1904166	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26678	0.81[YRI][hapmap]
rs27646	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35233	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35234	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs460741	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs6450097	0.94[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	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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52284800-52288200	Active TSS	NHLF	lung
2	chr5:52285800-52288200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:52286200-52289000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:52286200-52295400	Weak transcription	Pancreas	Pancrea
5	chr5:52286200-52300400	Weak transcription	Gastric	stomach
6	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
7	chr5:52286200-52313600	Weak transcription	Lung	lung
8	chr5:52286400-52288200	Flanking Active TSS	HUVEC	blood vessel
9	chr5:52286400-52289000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:52286600-52289400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:52286600-52289400	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:52286600-52291000	Weak transcription	Esophagus	oesophagus
13	chr5:52286600-52292000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:52286600-52292600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:52286600-52293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
18	chr5:52286800-52290400	Transcr. at gene 5' and 3'	NHEK	skin
19	chr5:52286800-52294400	Weak transcription	Osteobl	bone
20	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
21	chr5:52287000-52291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:52287000-52292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:52287000-52293000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:52287000-52293400	Weak transcription	Fetal Intestine Small	intestine
25	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:52287200-52288200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:52287200-52288200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:52287200-52288400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr5:52287200-52288400	Weak transcription	NH-A	brain
30	chr5:52287200-52292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:52287200-52293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:52287200-52293400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:52287200-52293600	Weak transcription	Fetal Kidney	kidney
34	chr5:52287400-52288400	Weak transcription	A549	lung
35	chr5:52287400-52289600	Enhancers	Brain Hippocampus Middle	brain
36	chr5:52287600-52288200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:52287600-52288200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:52287600-52288200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:52287600-52290800	Transcr. at gene 5' and 3'	HMEC	breast
40	chr5:52287800-52288400	Weak transcription	Brain Substantia Nigra	brain
41	chr5:52287800-52288600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:52287800-52288800	Weak transcription	NHDF-Ad	bronchial
43	chr5:52288000-52288200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr5:52288000-52288200	Flanking Active TSS	HepG2	liver
45	chr5:52288000-52288600	Transcr. at gene 5' and 3'	Hela-S3	cervix
46	chr5:52288000-52292400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast

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