Variant report

Variant	rs55853418
Chromosome Location	chr3:119233265-119233266
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119182245..119183869-chr3:119232847..119235676,2	MCF-7	breast:
2	chr3:119231563..119234574-chr3:119234818..119238744,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11539377	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915398	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916488	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11917446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917642	0.85[EUR][1000 genomes]
rs11918271	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919404	0.85[EUR][1000 genomes]
rs11919541	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919760	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11921098	0.85[EUR][1000 genomes]
rs11922005	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11923882	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11925305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829840	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16829878	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16829888	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3732414	0.85[EUR][1000 genomes]
rs503083	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55696355	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55968892	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56149432	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56195264	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56413426	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56710033	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57168946	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57389809	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57935532	0.95[EUR][1000 genomes]
rs58398719	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58639515	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58843212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58978800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59482964	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60006470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438533	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6762095	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6763716	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6764495	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776387	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777140	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6779137	0.85[EUR][1000 genomes]
rs6783100	0.85[EUR][1000 genomes]
rs6802790	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6808654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810215	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs716649	0.85[EUR][1000 genomes]
rs72952928	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72952932	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72952934	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72952950	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72970333	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72970352	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73857028	0.89[EUR][1000 genomes]
rs7621149	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7626731	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642792	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7650975	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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 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	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
2	chr3:119218600-119234400	Weak transcription	Colonic Mucosa	Colon
3	chr3:119218600-119236600	Weak transcription	Esophagus	oesophagus
4	chr3:119219000-119235800	Weak transcription	Fetal Kidney	kidney
5	chr3:119219400-119236800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:119219600-119237000	Weak transcription	Small Intestine	intestine
7	chr3:119219800-119233600	Weak transcription	Ovary	ovary
8	chr3:119219800-119235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:119219800-119239200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
12	chr3:119220800-119243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:119221000-119244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:119221200-119243600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:119221200-119244400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
17	chr3:119221600-119237400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:119221600-119244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:119225200-119235000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:119225400-119233400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:119225400-119233600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:119225400-119234000	Weak transcription	Gastric	stomach
25	chr3:119225400-119236000	Weak transcription	Pancreas	Pancrea
26	chr3:119225400-119236600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:119226000-119236800	Weak transcription	Right Ventricle	heart
28	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:119226000-119245200	Strong transcription	Liver	Liver
30	chr3:119226600-119245200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:119227000-119235800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:119227000-119236800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:119227000-119239800	Weak transcription	Psoas Muscle	Psoas
34	chr3:119227400-119245400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:119227600-119235200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:119227600-119236000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:119227800-119233600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:119227800-119234000	Weak transcription	K562	blood
39	chr3:119227800-119235600	Weak transcription	Brain Angular Gyrus	brain
40	chr3:119227800-119235800	Weak transcription	HUVEC	blood vessel
41	chr3:119227800-119236000	Weak transcription	Thymus	Thymus
42	chr3:119228000-119233600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:119228000-119234600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:119228000-119243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:119229000-119236000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:119229200-119240200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:119229200-119244600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:119229400-119237000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:119229800-119234000	Weak transcription	Rectal Mucosa Donor 31	rectum

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