Variant report

Variant	rs55968892
Chromosome Location	chr3:119239676-119239677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11539377	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11915398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916272	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916344	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917446	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11917642	0.85[EUR][1000 genomes]
rs11918271	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919404	0.85[EUR][1000 genomes]
rs11919541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919760	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11921098	0.85[EUR][1000 genomes]
rs11922005	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923882	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11925305	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16829840	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16829878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732414	0.85[EUR][1000 genomes]
rs503083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55696355	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55853418	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56149432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56195264	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56413426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56710033	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57168946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57389809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57935532	0.95[EUR][1000 genomes]
rs58398719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639515	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58843212	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58978800	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59482964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60006470	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762095	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6763716	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764495	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775021	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6776387	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779137	0.85[EUR][1000 genomes]
rs6783100	0.85[EUR][1000 genomes]
rs6802790	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6808654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6810215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716649	0.85[EUR][1000 genomes]
rs72952928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72970333	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72970352	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73857028	0.89[EUR][1000 genomes]
rs7621149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626731	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642119	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650975	0.89[EUR][1000 genomes];1.00[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
3	chr3:119220800-119243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:119221000-119244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:119221200-119243600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:119221200-119244400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
8	chr3:119221600-119244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119226000-119245200	Strong transcription	Liver	Liver
13	chr3:119226600-119245200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:119227000-119239800	Weak transcription	Psoas Muscle	Psoas
15	chr3:119227400-119245400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:119228000-119243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:119229200-119240200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:119229200-119244600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:119230600-119245400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr3:119230800-119244400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:119231200-119244000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:119231600-119240000	Strong transcription	HSMM	muscle
24	chr3:119231600-119240000	Strong transcription	Osteobl	bone
25	chr3:119231600-119240600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:119231600-119243400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:119231800-119240200	Strong transcription	Primary T cells from cord blood	blood
28	chr3:119231800-119240200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:119231800-119240200	Strong transcription	Fetal Brain Male	brain
30	chr3:119231800-119240600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:119231800-119240800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:119231800-119243200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:119231800-119243400	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr3:119231800-119244000	Strong transcription	Adipose Nuclei	Adipose
35	chr3:119231800-119244800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:119231800-119245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood
38	chr3:119232000-119240200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:119232000-119243200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:119232000-119244200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:119232000-119244200	Strong transcription	Brain Substantia Nigra	brain
42	chr3:119232000-119245200	Strong transcription	A549	lung
43	chr3:119232200-119243200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:119233000-119239800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:119233000-119240000	Strong transcription	Brain Hippocampus Middle	brain
46	chr3:119233000-119245200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:119233200-119243600	Strong transcription	Brain Anterior Caudate	brain
48	chr3:119233200-119244600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr3:119233400-119240400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:119234200-119241200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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