Variant report

Variant	rs2272489
Chromosome Location	chr3:160253729-160253730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160251582..160254432-chr3:160256598..160258319,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1141023	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236389	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236452	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236487	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17826161	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882124	0.87[ASN][1000 genomes]
rs1882128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1920648	0.87[ASN][1000 genomes]
rs1920654	0.87[ASN][1000 genomes]
rs1979160	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2029361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41272955	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41272957	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4254702	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4434183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679883	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679887	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680577	0.96[ASN][1000 genomes]
rs4680582	0.88[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55853078	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56051094	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322040	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776582	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780828	0.87[ASN][1000 genomes]
rs6806971	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154549	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154552	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154567	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154591	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154596	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154600	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154602	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155903	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155920	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155922	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155924	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622031	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826290	0.96[ASN][1000 genomes]
rs9845172	0.87[ASN][1000 genomes]
rs9847144	0.87[ASN][1000 genomes]
rs9876980	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 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	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:160217200-160254000	Strong transcription	Dnd41	blood
10	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
12	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
13	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
14	chr3:160229200-160254000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:160229200-160254000	Strong transcription	Placenta	Placenta
16	chr3:160229800-160253800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:160230000-160254000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:160230600-160254600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:160231000-160254400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:160234200-160258200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:160234600-160261000	Weak transcription	Spleen	Spleen
22	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
23	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
24	chr3:160236600-160254000	Strong transcription	Hela-S3	cervix
25	chr3:160239600-160265200	Weak transcription	Brain Substantia Nigra	brain
26	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:160241000-160256400	Weak transcription	Psoas Muscle	Psoas
28	chr3:160241800-160254200	Strong transcription	HMEC	breast
29	chr3:160241800-160255600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:160244400-160263400	Weak transcription	Small Intestine	intestine
32	chr3:160244800-160256800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:160244800-160259600	Weak transcription	Brain Angular Gyrus	brain
34	chr3:160245000-160254600	Weak transcription	Brain Anterior Caudate	brain
35	chr3:160245000-160258400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:160245000-160259800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:160245200-160262200	Weak transcription	Fetal Kidney	kidney
38	chr3:160245800-160255200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:160246400-160254800	Weak transcription	Colonic Mucosa	Colon
40	chr3:160246600-160254000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:160246800-160266400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:160247000-160258400	Weak transcription	HSMMtube	muscle
44	chr3:160247000-160259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:160247000-160261000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
48	chr3:160248400-160261200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:160248400-160261200	Weak transcription	Gastric	stomach
50	chr3:160248400-160261200	Weak transcription	Lung	lung

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