Variant report

Variant	rs62406187
Chromosome Location	chr5:179185686-179185687
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179182800..179186679-chr5:179187040..179189568,4	K562	blood:
2	chr5:179159135..179161287-chr5:179183499..179187060,3	MCF-7	breast:
3	chr5:179183781..179185717-chr5:179193398..179195095,2	K562	blood:
4	chr5:179182162..179184626-chr5:179184667..179187247,2	MCF-7	breast:
5	chr5:179185380..179186978-chr5:179232551..179234204,2	MCF-7	breast:
6	chr5:179180262..179181964-chr5:179184888..179186851,2	K562	blood:
7	chr5:179185016..179191633-chr5:179218101..179224928,12	MCF-7	breast:
8	chr5:179180262..179182416-chr5:179184220..179186388,2	K562	blood:
9	chr5:179184236..179186610-chr5:179249273..179251326,2	K562	blood:
10	chr5:179158546..179161718-chr5:179184592..179191275,7	MCF-7	breast:
11	chr5:179125096..179127519-chr5:179185034..179186822,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161021	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11738269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738720	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740569	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741570	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743232	0.84[ASN][1000 genomes]
rs11744616	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746924	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11747496	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12522263	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469020	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469021	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17617068	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17617710	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34057110	0.88[ASN][1000 genomes]
rs3756614	0.94[ASN][1000 genomes]
rs3797762	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797776	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41458244	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700838	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700840	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55654737	0.97[ASN][1000 genomes]
rs55827522	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55975622	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56309143	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56335144	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58386410	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404347	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406176	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406177	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406178	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62406181	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406219	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406223	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406228	0.82[AMR][1000 genomes]
rs6601067	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601072	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6639	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6860716	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893300	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6895902	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72807339	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs730012	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7444006	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7447159	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7704520	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705530	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715356	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7734102	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7735702	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
2	chr5:179162000-179186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:179162000-179186000	Weak transcription	HSMM	muscle
4	chr5:179162000-179186200	Weak transcription	HMEC	breast
5	chr5:179162000-179186600	Weak transcription	Hela-S3	cervix
6	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:179162600-179189000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:179164600-179186600	Weak transcription	NH-A	brain
9	chr5:179165800-179188800	Weak transcription	Brain Germinal Matrix	brain
10	chr5:179167000-179186600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:179167200-179188800	Weak transcription	NHEK	skin
12	chr5:179168000-179185800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:179171800-179188800	Weak transcription	Colonic Mucosa	Colon
14	chr5:179174400-179186600	Weak transcription	Esophagus	oesophagus
15	chr5:179174400-179192200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:179177000-179188800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:179177200-179186600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:179177400-179186200	Weak transcription	HSMMtube	muscle
19	chr5:179177400-179187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:179177800-179186000	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:179177800-179188800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:179178000-179186000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:179178000-179186800	Weak transcription	Placenta	Placenta
24	chr5:179178000-179187000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:179178000-179188600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:179178000-179188600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:179178000-179188800	Weak transcription	Osteobl	bone
28	chr5:179178400-179186400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:179178600-179186200	Weak transcription	Dnd41	blood
30	chr5:179178600-179186600	Weak transcription	Thymus	Thymus
31	chr5:179179000-179185800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:179179000-179186000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:179179000-179186800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:179179000-179189200	Weak transcription	Fetal Brain Female	brain
35	chr5:179181000-179186600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:179181600-179187000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:179182000-179186600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:179182200-179186200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:179182200-179188600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:179182200-179188600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:179182400-179186000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:179182400-179186000	Weak transcription	Aorta	Aorta
43	chr5:179182400-179186000	Weak transcription	Right Atrium	heart
44	chr5:179182400-179186000	Weak transcription	A549	lung
45	chr5:179182400-179186000	Weak transcription	GM12878-XiMat	blood
46	chr5:179182400-179186200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:179182400-179186200	Weak transcription	Brain Substantia Nigra	brain
48	chr5:179182400-179186400	Weak transcription	Brain Angular Gyrus	brain
49	chr5:179182400-179186800	Weak transcription	Psoas Muscle	Psoas
50	chr5:179182400-179187200	Weak transcription	Lung	lung

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