Variant report

Variant	rs62357227
Chromosome Location	chr5:52303286-52303287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52283964..52286344-chr5:52303235..52304989,2	MCF-7	breast:
2	chr5:52287901..52290762-chr5:52300870..52303377,2	MCF-7	breast:
3	chr5:52299602..52301517-chr5:52301947..52304132,2	MCF-7	breast:
4	chr5:52298353..52300154-chr5:52302167..52303725,2	K562	blood:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16876270	0.86[EUR][1000 genomes]
rs3212394	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41305896	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56719416	0.90[EUR][1000 genomes]
rs62357159	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62357175	0.86[EUR][1000 genomes]
rs62357177	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62357195	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357197	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357199	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357200	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357202	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357203	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357230	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6450105	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
2	chr5:52286200-52313600	Weak transcription	Lung	lung
3	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:52293600-52304000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:52293800-52313400	Weak transcription	Fetal Intestine Small	intestine
6	chr5:52298800-52303400	Enhancers	Dnd41	blood
7	chr5:52299000-52304800	Genic enhancers	HepG2	liver
8	chr5:52299400-52313400	Weak transcription	Esophagus	oesophagus
9	chr5:52299800-52305000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr5:52299800-52306000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:52300200-52304800	Weak transcription	Fetal Intestine Large	intestine
12	chr5:52300200-52305200	Enhancers	A549	lung
13	chr5:52301200-52306800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:52301600-52303600	Enhancers	Brain Cingulate Gyrus	brain
15	chr5:52301600-52303600	Enhancers	Brain Substantia Nigra	brain
16	chr5:52302000-52304600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:52302000-52304600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:52302200-52305400	Enhancers	NH-A	brain
19	chr5:52302400-52303400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:52302400-52303400	Flanking Active TSS	NHEK	skin
21	chr5:52302400-52303800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:52302400-52305200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:52302400-52305200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr5:52302400-52306000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:52302600-52303400	Flanking Active TSS	NHDF-Ad	bronchial
26	chr5:52302600-52305000	Enhancers	Osteobl	bone
27	chr5:52302600-52308000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:52302800-52303800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:52302800-52304800	Weak transcription	Brain Angular Gyrus	brain
30	chr5:52302800-52305000	Enhancers	HUVEC	blood vessel
31	chr5:52302800-52305400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:52303000-52305000	Enhancers	NHLF	lung
33	chr5:52303000-52305400	Enhancers	Hela-S3	cervix
34	chr5:52303000-52307400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:52303200-52303400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:52303200-52303400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:52303200-52303400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:52303200-52303400	Enhancers	Fetal Brain Male	brain
39	chr5:52303200-52303400	Enhancers	Rectal Smooth Muscle	rectum
40	chr5:52303200-52304000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:52303200-52304000	Weak transcription	Brain Anterior Caudate	brain
42	chr5:52303200-52304800	Genic enhancers	HMEC	breast
43	chr5:52303200-52305800	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:52303200-52306800	Weak transcription	Stomach Smooth Muscle	stomach

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