Variant report

Variant	rs1045920
Chromosome Location	chr2:55771169-55771170
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10172181	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10172506	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10173150	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10182131	0.89[AMR][1000 genomes]
rs10194634	0.84[AMR][1000 genomes]
rs10195281	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10200159	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10203953	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10204169	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10496044	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11676573	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11902712	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12615063	0.89[AMR][1000 genomes]
rs12616502	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616982	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12623625	0.89[AMR][1000 genomes]
rs13016772	0.82[AFR][1000 genomes]
rs13028892	0.88[AFR][1000 genomes]
rs13382187	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13383352	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13399762	0.94[AMR][1000 genomes]
rs13400946	0.89[AMR][1000 genomes]
rs13407344	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13420929	0.89[AMR][1000 genomes]
rs13428382	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13428486	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430684	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17047094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17047119	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867964	0.89[AMR][1000 genomes]
rs3748955	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816489	0.86[AFR][1000 genomes]
rs3974266	0.80[AFR][1000 genomes]
rs4233962	0.83[AFR][1000 genomes]
rs4671248	0.82[AFR][1000 genomes]
rs62165178	0.90[AFR][1000 genomes]
rs6545507	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545508	0.89[ASN][1000 genomes]
rs6545509	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545510	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545512	0.89[AMR][1000 genomes]
rs6545513	0.89[AMR][1000 genomes]
rs6705295	0.84[AMR][1000 genomes]
rs6712314	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6716100	0.81[AFR][1000 genomes]
rs6717574	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6725101	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6736996	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739788	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6745430	0.83[ASN][1000 genomes]
rs6760959	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs736345	0.83[ASN][1000 genomes]
rs7558127	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7567115	0.89[AMR][1000 genomes]
rs7575906	0.89[AMR][1000 genomes]
rs7582174	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586115	0.89[AMR][1000 genomes]
rs7586124	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586366	0.89[AMR][1000 genomes]
rs7594212	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7594497	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9309267	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309268	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9808054	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers 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	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
4	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
5	chr2:55748200-55772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:55748200-55773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:55748200-55777400	Weak transcription	NHLF	lung
9	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
10	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:55748400-55772200	Weak transcription	HMEC	breast
12	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
15	chr2:55753200-55772400	Weak transcription	HepG2	liver
16	chr2:55753400-55772200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:55754000-55774600	Weak transcription	Spleen	Spleen
19	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55754200-55772400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55754400-55772200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:55754400-55783000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:55758000-55771400	Weak transcription	NH-A	brain
24	chr2:55758200-55781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:55758200-55783800	Weak transcription	Gastric	stomach
26	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
27	chr2:55758400-55774000	Weak transcription	Hela-S3	cervix
28	chr2:55758400-55776000	Weak transcription	HUVEC	blood vessel
29	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:55759200-55772400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:55759600-55773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:55761200-55777200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:55761400-55781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:55762000-55772200	Weak transcription	Brain Germinal Matrix	brain
37	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:55762200-55771200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:55762200-55771200	Weak transcription	Lung	lung
40	chr2:55762200-55771800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:55762200-55773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:55762200-55782600	Weak transcription	NHEK	skin
43	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart
44	chr2:55762800-55781000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:55763000-55771600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55763800-55773600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:55764400-55771400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:55765000-55771200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:55765000-55771200	Weak transcription	Ovary	ovary
50	chr2:55765000-55771200	Weak transcription	Thymus	Thymus

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