Variant report

Variant	rs11024690
Chromosome Location	chr11:18525008-18525009
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	chr11:18523134..18525555-chr11:18546904..18549561,3	K562	blood:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10500836	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10741747	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10766483	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10766484	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10766485	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10832940	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024699	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024711	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12224694	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12225037	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419063	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12574808	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12577346	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1395319	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1395320	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34457574	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3925781	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4298881	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4623881	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756949	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756950	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756952	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56333121	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6486434	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105889	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7107057	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7931630	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7934817	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7951508	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952284	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs868069	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11024690	TSG101	cis	Esophagus Mucosa	GTEx
rs11024690	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs11024690	TSG101	cis	Muscle Skeletal	GTEx
rs11024690	LDHC	cis	Thyroid	GTEx

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	chr11:18510800-18541400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr11:18511800-18527000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:18512800-18526800	Weak transcription	Spleen	Spleen
17	chr11:18513000-18526800	Weak transcription	Pancreas	Pancrea
18	chr11:18513000-18544000	Weak transcription	Gastric	stomach
19	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
20	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:18513200-18525400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:18513200-18532600	Weak transcription	Esophagus	oesophagus
23	chr11:18514600-18540800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:18514800-18539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:18515000-18537600	Strong transcription	Fetal Thymus	thymus
26	chr11:18515000-18540000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:18515000-18540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:18515200-18538000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
30	chr11:18515600-18537600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr11:18515600-18537800	Strong transcription	Fetal Intestine Large	intestine
32	chr11:18516200-18538200	Strong transcription	Adipose Nuclei	Adipose
33	chr11:18516200-18538800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr11:18516200-18540400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:18516400-18531400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:18516400-18532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:18516400-18540400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:18516800-18541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:18517200-18540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:18517600-18534200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr11:18518000-18539200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:18518200-18525400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:18518200-18538600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:18518200-18540400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:18518400-18530400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:18518600-18528800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:18518600-18531800	Weak transcription	Aorta	Aorta
48	chr11:18518600-18537200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:18519200-18525600	Strong transcription	NHDF-Ad	bronchial
50	chr11:18519200-18527000	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links