Variant report

Variant	rs62406177
Chromosome Location	chr5:179164209-179164210
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
2	chr5:179103926..179106579-chr5:179164201..179165877,2	K562	blood:
3	chr5:179124528..179127289-chr5:179163216..179165025,3	K562	blood:
4	chr5:179157089..179164271-chr5:179242384..179250347,16	K562	blood:
5	chr5:179158557..179162046-chr5:179162635..179164608,3	K562	blood:
6	chr5:179161775..179164271-chr5:179248764..179250347,2	K562	blood:
7	chr5:179161374..179164232-chr5:179220024..179222829,2	MCF-7	breast:
8	chr5:179143486..179153989-chr5:179156108..179164461,19	MCF-7	breast:
9	chr5:179037382..179039814-chr5:179164191..179166934,2	K562	blood:
10	chr5:179163103..179164618-chr5:179497760..179499779,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161011	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11738269	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11738720	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739042	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740569	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11741570	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11743232	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11744616	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11746924	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11747496	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12522263	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469020	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1469021	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17617068	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17617710	0.90[ASN][1000 genomes]
rs3756614	0.84[ASN][1000 genomes]
rs3797762	0.90[ASN][1000 genomes]
rs3797776	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41458244	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4700838	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4700840	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55654737	0.87[ASN][1000 genomes]
rs55827522	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55975622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56309143	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56335144	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58386410	0.90[ASN][1000 genomes]
rs62404347	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406176	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406178	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406181	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406187	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406219	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406223	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6601067	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6601072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6639	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6887507	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6893300	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6895902	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72807339	0.81[AMR][1000 genomes]
rs730012	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7444006	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7447159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7704520	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7705530	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7709723	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7715356	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7734102	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7735702	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179161000-179164600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:179161000-179174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:179161000-179174000	Weak transcription	Gastric	stomach
4	chr5:179161000-179174200	Weak transcription	Esophagus	oesophagus
5	chr5:179161000-179181200	Weak transcription	Aorta	Aorta
6	chr5:179161000-179181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179161000-179181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:179161200-179166000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:179161400-179165600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr5:179161600-179164800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:179161600-179165000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:179161600-179165400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:179161600-179176600	Weak transcription	HSMMtube	muscle
14	chr5:179161800-179164400	Enhancers	Left Ventricle	heart
15	chr5:179161800-179164800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:179161800-179165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:179161800-179166000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:179161800-179166400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:179161800-179174200	Weak transcription	A549	lung
20	chr5:179161800-179176600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:179161800-179176800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:179161800-179177400	Weak transcription	Fetal Kidney	kidney
23	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
24	chr5:179162000-179164600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:179162000-179165000	Enhancers	Brain Anterior Caudate	brain
26	chr5:179162000-179165400	Weak transcription	NHEK	skin
27	chr5:179162000-179165800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:179162000-179166200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr5:179162000-179166800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179162000-179168200	Weak transcription	Psoas Muscle	Psoas
31	chr5:179162000-179168600	Strong transcription	Fetal Stomach	stomach
32	chr5:179162000-179174000	Weak transcription	Liver	Liver
33	chr5:179162000-179176600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:179162000-179176600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:179162000-179176600	Weak transcription	Osteobl	bone
36	chr5:179162000-179176800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:179162000-179181200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:179162000-179181400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:179162000-179181800	Weak transcription	NHLF	lung
40	chr5:179162000-179186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:179162000-179186000	Weak transcription	HSMM	muscle
42	chr5:179162000-179186200	Weak transcription	HMEC	breast
43	chr5:179162000-179186600	Weak transcription	Hela-S3	cervix
44	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:179162200-179166000	Weak transcription	Fetal Intestine Large	intestine
46	chr5:179162400-179164600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr5:179162600-179165600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr5:179162600-179166000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:179162600-179189000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr5:179162800-179164400	Genic enhancers	K562	blood

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