Variant report

Variant	rs2055558
Chromosome Location	chr3:105562247-105562248
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12054270	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487349	0.82[ASN][1000 genomes]
rs12493071	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503923	0.87[AMR][1000 genomes]
rs16851512	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851553	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851673	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851705	0.87[AMR][1000 genomes]
rs16851706	0.87[AMR][1000 genomes]
rs16851707	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814078	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867194	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028598	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028599	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120104	0.88[ASN][1000 genomes]
rs2301028	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301034	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301035	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213928	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34360428	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35909361	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772517	0.90[ASN][1000 genomes]
rs3772522	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772525	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821490	0.88[ASN][1000 genomes]
rs4431143	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4469007	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894956	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255570	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255572	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255573	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255575	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62256353	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62258160	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261460	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261462	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261487	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261489	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261491	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261492	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261493	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261495	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261496	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261497	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261498	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261499	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261538	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261539	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263056	0.87[ASN][1000 genomes]
rs62263057	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263059	0.87[ASN][1000 genomes]
rs62263169	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263170	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264260	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6809776	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619706	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628896	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7631219	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641527	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650046	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964173	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9657903	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657924	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971109	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849559	0.88[ASN][1000 genomes]
rs9856147	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv508234	chr3:105549864-105565806	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
2	chr3:105532200-105563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:105533800-105570000	Weak transcription	Dnd41	blood
4	chr3:105534200-105566200	Weak transcription	Brain Germinal Matrix	brain
5	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
6	chr3:105542600-105566000	Weak transcription	Fetal Stomach	stomach
7	chr3:105543400-105581200	Weak transcription	Gastric	stomach
8	chr3:105543800-105571000	Weak transcription	Lung	lung
9	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
11	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:105549200-105564400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:105550000-105562600	Weak transcription	HUVEC	blood vessel
14	chr3:105550000-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:105553400-105564000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:105554000-105566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:105555000-105562800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:105555000-105562800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:105555200-105566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:105555800-105564400	Weak transcription	HMEC	breast
21	chr3:105555800-105565800	Weak transcription	Right Atrium	heart
22	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
23	chr3:105556200-105562800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:105556200-105566600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:105556200-105570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:105556200-105571600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
28	chr3:105556400-105562800	Weak transcription	Brain Anterior Caudate	brain
29	chr3:105556400-105562800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:105556400-105562800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:105556400-105562800	Weak transcription	Fetal Kidney	kidney
32	chr3:105556400-105565400	Weak transcription	NHLF	lung
33	chr3:105556400-105565600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:105556400-105566200	Weak transcription	Fetal Heart	heart
35	chr3:105556400-105568000	Weak transcription	HSMM	muscle
36	chr3:105556600-105569600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:105556600-105569800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:105556800-105562800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:105556800-105562800	Weak transcription	Small Intestine	intestine
40	chr3:105556800-105563600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:105557000-105562600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:105557000-105562600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:105557000-105562800	Weak transcription	Fetal Lung	lung
44	chr3:105557000-105563000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:105557000-105565400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:105557400-105563600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:105557600-105563000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:105557800-105562800	Weak transcription	Ovary	ovary
49	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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