Variant report

Variant	rs28720674
Chromosome Location	chr5:61648323-61648324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61601612..61603523-chr5:61647478..61650855,3	MCF-7	breast:
2	chr5:61645079..61646734-chr5:61646742..61649036,2	K562	blood:
3	chr5:61604639..61607587-chr5:61647579..61650088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10079409	0.89[ASN][1000 genomes]
rs1025032	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10471542	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1054897	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10939936	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10939938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153750	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12519766	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658256	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16890656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1808400	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1848504	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2063256	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2272290	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2463078	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264522	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs264525	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs264526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs264529	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37032	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3842912	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3846468	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3857259	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3892140	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700491	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863617	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864450	0.88[ASN][1000 genomes]
rs6872078	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6884054	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73104056	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73104058	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729719	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734679	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9291759	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9981	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
2	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
3	chr5:61607800-61669400	Weak transcription	NHLF	lung
4	chr5:61610200-61658600	Weak transcription	Ovary	ovary
5	chr5:61612000-61661000	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:61615600-61658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:61618400-61658600	Weak transcription	Hela-S3	cervix
8	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:61622600-61658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:61623800-61658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:61628800-61652000	Weak transcription	Fetal Brain Female	brain
13	chr5:61629200-61676400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:61629600-61665000	Weak transcription	Esophagus	oesophagus
15	chr5:61629800-61659400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:61631000-61658400	Weak transcription	Colonic Mucosa	Colon
17	chr5:61631200-61658800	Weak transcription	Pancreas	Pancrea
18	chr5:61631200-61669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:61631200-61669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:61631200-61676000	Weak transcription	Lung	lung
21	chr5:61631400-61648400	Weak transcription	Liver	Liver
22	chr5:61631400-61660000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:61632400-61650400	Weak transcription	A549	lung
24	chr5:61635000-61650600	Weak transcription	Brain Germinal Matrix	brain
25	chr5:61635200-61648400	Weak transcription	NH-A	brain
26	chr5:61635200-61651800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:61637000-61649600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:61637800-61648400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:61638600-61671200	Weak transcription	Small Intestine	intestine
30	chr5:61639600-61658600	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:61639800-61651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:61639800-61684200	Weak transcription	Psoas Muscle	Psoas
33	chr5:61641200-61657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:61641400-61658600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:61641400-61682400	Weak transcription	Fetal Heart	heart
36	chr5:61642200-61649400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:61642400-61665400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:61642600-61656000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:61642600-61660800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:61642600-61688400	Weak transcription	Right Ventricle	heart
42	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:61642600-61699200	Weak transcription	Gastric	stomach
44	chr5:61642800-61648400	Weak transcription	Fetal Lung	lung
45	chr5:61642800-61654000	Weak transcription	Brain Substantia Nigra	brain
46	chr5:61642800-61659000	Weak transcription	HepG2	liver
47	chr5:61643000-61650600	Weak transcription	NHEK	skin
48	chr5:61643000-61657600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:61643000-61658600	Weak transcription	Brain Angular Gyrus	brain
50	chr5:61643000-61658600	Weak transcription	Stomach Smooth Muscle	stomach

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