Variant report

Variant	rs11739042
Chromosome Location	chr5:179182495-179182496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179182162..179184626-chr5:179184667..179187247,2	MCF-7	breast:
2	chr5:179159546..179161404-chr5:179180991..179182932,2	MCF-7	breast:
3	chr5:179181804..179184029-chr5:179232309..179234271,2	MCF-7	breast:
4	chr5:179175737..179178528-chr5:179180784..179182506,2	MCF-7	breast:
5	chr5:179159538..179161927-chr5:179181625..179183408,2	MCF-7	breast:
6	chr5:179180060..179181827-chr5:179182404..179185142,2	MCF-7	breast:

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

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

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

rs_ID	r²[population]
rs11738269	1.00[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]
rs11740569	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741570	0.91[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	1.00[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]
rs62406187	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406219	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406223	0.90[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	0.90[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:3 , 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

No data

Chromatin state (count:123 , 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	chr5:179165400-179184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:179165800-179188800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:179167000-179186600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:179167200-179188800	Weak transcription	NHEK	skin
13	chr5:179168000-179185800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:179171800-179188800	Weak transcription	Colonic Mucosa	Colon
15	chr5:179174400-179186600	Weak transcription	Esophagus	oesophagus
16	chr5:179174400-179192200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:179177000-179188800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:179177200-179186600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:179177400-179186200	Weak transcription	HSMMtube	muscle
20	chr5:179177400-179187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:179177800-179186000	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:179177800-179188800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:179178000-179186000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:179178000-179186800	Weak transcription	Placenta	Placenta
25	chr5:179178000-179187000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:179178000-179188600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:179178000-179188600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:179178000-179188800	Weak transcription	Osteobl	bone
29	chr5:179178400-179186400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:179178600-179186200	Weak transcription	Dnd41	blood
31	chr5:179178600-179186600	Weak transcription	Thymus	Thymus
32	chr5:179179000-179185800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:179179000-179186000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:179179000-179186800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:179179000-179189200	Weak transcription	Fetal Brain Female	brain
36	chr5:179179600-179182600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr5:179179800-179182600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr5:179180200-179182600	Enhancers	Duodenum Mucosa	Duodenum
39	chr5:179180200-179182800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr5:179180400-179182600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:179180400-179182600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr5:179180400-179182600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr5:179180400-179182600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr5:179180600-179182600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr5:179180600-179182600	Enhancers	Right Ventricle	heart
46	chr5:179180600-179182800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr5:179180600-179182800	Enhancers	Primary T cells from cord blood	blood
48	chr5:179180600-179182800	Enhancers	Pancreas	Pancrea
49	chr5:179180600-179183000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:179180600-179183000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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