Variant report

Variant	rs2284452
Chromosome Location	chr11:4156106-4156107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:4149701..4154222-chr11:4154719..4157955,5	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1015998	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835613	0.84[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs10835632	0.81[AMR][1000 genomes]
rs10835650	0.83[AMR][1000 genomes]
rs11030842	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs11030976	0.86[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs11030980	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11031043	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11031062	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11031070	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372804	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs1662161	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1662172	0.84[MEX][hapmap]
rs1662173	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs183484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980412	0.89[ASW][hapmap];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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119986	0.81[AMR][1000 genomes]
rs232054	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2735689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2735691	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920144	0.81[CHD][hapmap]
rs2923945	0.81[CHB][hapmap]
rs2959056	0.86[CHB][hapmap]
rs2959070	0.90[CHB][hapmap]
rs2959075	0.90[CHB][hapmap]
rs34356743	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794049	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910913	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910914	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs54816	0.83[AMR][1000 genomes]
rs67074167	0.81[AMR][1000 genomes]
rs725518	0.84[CHD][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs725519	0.84[CHD][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs9937	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1053189	chr11:4123119-4359044	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1048590	chr11:4133055-4225100	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv540911	chr11:4133055-4225100	Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1053482	chr11:4138062-4276133	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2284452	RRM1	cis	cerebellum	SCAN
rs2284452	TRIM21	cis	cerebellum	SCAN
rs2284452	OR51E2	cis	cerebellum	SCAN
rs2284452	OR52I2	cis	parietal	SCAN
rs2284452	TRIM5	cis	cerebellum	SCAN
rs2284452	KRTAP5-4	cis	cerebellum	SCAN
rs2284452	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4117800-4160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:4118000-4159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:4118400-4156200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:4119400-4157600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:4121000-4159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:4122400-4158000	Strong transcription	Dnd41	blood
7	chr11:4122800-4158000	Strong transcription	Fetal Thymus	thymus
8	chr11:4123000-4157600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:4123000-4157600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:4123000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:4123200-4158000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr11:4124000-4157600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:4124000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:4126600-4166600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:4127600-4158000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:4131000-4157400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:4137400-4156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:4137800-4158000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:4138200-4160600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:4138600-4157600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:4138600-4158000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr11:4138800-4157400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr11:4138800-4158000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:4138800-4160400	Strong transcription	Placenta	Placenta
25	chr11:4139600-4157400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:4139800-4158000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:4140400-4157400	Strong transcription	Fetal Lung	lung
28	chr11:4140400-4157600	Strong transcription	K562	blood
29	chr11:4140400-4158000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:4141000-4156200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:4143200-4159400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:4144000-4159400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr11:4144200-4158000	Strong transcription	GM12878-XiMat	blood
34	chr11:4144800-4160800	Weak transcription	Colonic Mucosa	Colon
35	chr11:4145400-4158200	Weak transcription	Esophagus	oesophagus
36	chr11:4145600-4157400	Weak transcription	Small Intestine	intestine
37	chr11:4145600-4159400	Weak transcription	Fetal Heart	heart
38	chr11:4147200-4158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:4147400-4156400	Weak transcription	Fetal Kidney	kidney
40	chr11:4148400-4159200	Weak transcription	Fetal Brain Male	brain
41	chr11:4148600-4164800	Weak transcription	HSMMtube	muscle
42	chr11:4148800-4165200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:4149200-4156400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:4149200-4159400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:4149200-4159400	Weak transcription	Brain Anterior Caudate	brain
46	chr11:4149200-4159600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:4149200-4160600	Weak transcription	Spleen	Spleen
48	chr11:4149200-4164600	Weak transcription	Gastric	stomach
49	chr11:4149400-4156400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:4149400-4162200	Weak transcription	Psoas Muscle	Psoas

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