Variant report

Variant	rs2658552
Chromosome Location	chr11:18524208-18524209
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	chr11:18523134..18525555-chr11:18546904..18549561,3	K562	blood:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10500836	0.93[JPT][hapmap]
rs10741745	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741746	0.87[ASN][1000 genomes]
rs10832940	0.85[JPT][hapmap]
rs10832941	0.86[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024694	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024711	0.86[JPT][hapmap]
rs11024717	0.89[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12224694	0.85[JPT][hapmap]
rs12361289	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419063	0.93[JPT][hapmap]
rs1395319	0.85[JPT][hapmap]
rs1395320	0.86[JPT][hapmap]
rs1857907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132302	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291752	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643866	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658554	0.90[ASN][1000 genomes]
rs2658564	0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs2658567	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2698567	0.89[ASN][1000 genomes]
rs3925781	0.93[JPT][hapmap]
rs4298881	0.93[JPT][hapmap]
rs4756949	0.86[JPT][hapmap]
rs6486430	0.86[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6486434	0.86[JPT][hapmap]
rs7105889	0.86[JPT][hapmap]
rs7107057	0.86[JPT][hapmap]
rs7119085	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7129164	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928872	0.86[JPT][hapmap]
rs7931630	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2658552	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs2658552	TSG101	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18483600-18526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:18504000-18540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:18505200-18531800	Weak transcription	Fetal Brain Male	brain
10	chr11:18509000-18537600	Strong transcription	Liver	Liver
11	chr11:18509000-18540200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:18509000-18540600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:18509600-18540200	Strong transcription	Placenta	Placenta
14	chr11:18510800-18524400	Strong transcription	Dnd41	blood
15	chr11:18510800-18541400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:18511000-18524400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:18511800-18527000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:18512800-18526800	Weak transcription	Spleen	Spleen
19	chr11:18513000-18526800	Weak transcription	Pancreas	Pancrea
20	chr11:18513000-18544000	Weak transcription	Gastric	stomach
21	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
22	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:18513200-18525400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:18513200-18532600	Weak transcription	Esophagus	oesophagus
25	chr11:18514600-18540800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:18514800-18539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:18515000-18537600	Strong transcription	Fetal Thymus	thymus
28	chr11:18515000-18540000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:18515000-18540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:18515200-18538000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
32	chr11:18515600-18537600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:18515600-18537800	Strong transcription	Fetal Intestine Large	intestine
34	chr11:18516200-18524400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:18516200-18524600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:18516200-18524600	Strong transcription	Fetal Brain Female	brain
37	chr11:18516200-18538200	Strong transcription	Adipose Nuclei	Adipose
38	chr11:18516200-18538800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:18516200-18540400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:18516400-18531400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:18516400-18532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:18516400-18540400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:18516800-18541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:18517000-18524400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:18517000-18524400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:18517200-18524800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:18517200-18540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:18517600-18534200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr11:18518000-18539200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:18518200-18524600	Strong transcription	Stomach Smooth Muscle	stomach

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