Variant report

Variant	rs62406219
Chromosome Location	chr5:179211629-179211630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:179208821..179211974-chr5:179218731..179221222,3	MCF-7	breast:
2	chr5:179210097..179212795-chr5:179213653..179217175,3	MCF-7	breast:
3	chr5:179206337..179209276-chr5:179211151..179214245,3	K562	blood:
4	chr5:179210356..179212439-chr5:179227637..179229283,2	MCF-7	breast:
5	chr5:179201693..179205348-chr5:179210724..179213200,3	MCF-7	breast:
6	chr5:179210375..179212924-chr5:179213806..179215338,2	K562	blood:
7	chr5:179210986..179213138-chr5:179230551..179233215,3	K562	blood:
8	chr5:179209719..179212653-chr5:179217734..179221028,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction
ENSG00000213316	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11738269	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738720	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11739042	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740569	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741570	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743232	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11744616	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746924	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11747496	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12522263	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1469020	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469021	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17617068	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17617710	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34057110	0.88[ASN][1000 genomes]
rs3756614	0.94[ASN][1000 genomes]
rs3797762	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797776	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41458244	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700838	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700840	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55654737	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55827522	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55975622	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56309143	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56335144	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58386410	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404347	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62406176	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406177	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406178	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406181	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62406187	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406223	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601067	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601072	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6639	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6860716	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893300	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6895902	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72807339	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs730012	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7444006	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7447159	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7704520	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705530	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709723	0.81[AMR][1000 genomes]
rs7715356	0.86[ASN][1000 genomes]
rs7734102	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7735702	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179199800-179214000	Weak transcription	Fetal Brain Male	brain
2	chr5:179202000-179221800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:179203400-179211800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:179203400-179213400	Weak transcription	Psoas Muscle	Psoas
5	chr5:179203400-179218200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:179203400-179221600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:179203600-179219600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:179203600-179220400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:179203600-179222000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:179204000-179221200	Weak transcription	Small Intestine	intestine
11	chr5:179205000-179218800	Weak transcription	Right Atrium	heart
12	chr5:179205200-179220600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:179205200-179221800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:179206000-179220200	Weak transcription	Ovary	ovary
15	chr5:179206400-179214600	Weak transcription	HepG2	liver
16	chr5:179206400-179219200	Weak transcription	Gastric	stomach
17	chr5:179207000-179220200	Weak transcription	GM12878-XiMat	blood
18	chr5:179207200-179215200	Weak transcription	HSMMtube	muscle
19	chr5:179207200-179218600	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:179207200-179218800	Weak transcription	Adipose Nuclei	Adipose
21	chr5:179207200-179220600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:179207400-179212600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:179207400-179215200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:179207400-179218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:179207400-179219400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:179207400-179221000	Weak transcription	Brain Substantia Nigra	brain
27	chr5:179207600-179212000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:179207600-179212400	Weak transcription	Esophagus	oesophagus
29	chr5:179207600-179212600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:179207600-179213000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:179207600-179213400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:179207600-179218800	Weak transcription	Fetal Lung	lung
33	chr5:179207600-179219200	Weak transcription	Colonic Mucosa	Colon
34	chr5:179207600-179219400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:179207600-179219400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:179207600-179220000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:179207600-179220200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:179207600-179220200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:179207600-179220200	Weak transcription	Pancreas	Pancrea
40	chr5:179207600-179220600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:179207600-179220800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:179207600-179221200	Weak transcription	Fetal Intestine Large	intestine
43	chr5:179207600-179222200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:179207600-179222600	Weak transcription	Aorta	Aorta
45	chr5:179207800-179211800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:179207800-179215200	Weak transcription	Liver	Liver
47	chr5:179207800-179216200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:179207800-179218200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:179207800-179219200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:179207800-179220200	Weak transcription	Primary T cells fromperipheralblood	blood

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