Variant report

Variant	rs10741747
Chromosome Location	chr11:18586122-18586123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10500836	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10766483	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10766484	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10766485	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832940	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832941	0.84[JPT][hapmap]
rs11024690	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024699	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024711	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024717	0.93[JPT][hapmap]
rs12224694	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12225037	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419063	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12574808	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577346	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395319	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395320	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1857907	0.85[JPT][hapmap]
rs2132302	0.85[JPT][hapmap]
rs34457574	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3925781	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4298881	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4623881	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756949	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756950	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486434	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105889	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107057	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119085	0.92[JPT][hapmap]
rs7129164	0.85[JPT][hapmap]
rs7928872	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs7931630	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7934817	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7951508	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952284	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868069	0.89[EUR][1000 genomes];0.90[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	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
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv972915	chr11:18571883-18591969	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10741747	TSG101	cis	Muscle Skeletal	GTEx
rs10741747	TSG101	cis	Esophagus Mucosa	GTEx
rs10741747	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs10741747	TSG101	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549200-18591400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
4	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
6	chr11:18549800-18588200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:18549800-18592000	Weak transcription	NHLF	lung
8	chr11:18549800-18594400	Weak transcription	K562	blood
9	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:18550600-18591400	Weak transcription	Dnd41	blood
11	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:18558400-18592200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:18559200-18592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
15	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:18564000-18586400	Weak transcription	GM12878-XiMat	blood
18	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:18567200-18594600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
22	chr11:18567800-18588200	Strong transcription	Adipose Nuclei	Adipose
23	chr11:18568600-18591000	Weak transcription	HMEC	breast
24	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:18572000-18588200	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:18574600-18592200	Strong transcription	Liver	Liver
29	chr11:18574800-18588600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:18575000-18588200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr11:18575800-18590000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:18576200-18590200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:18576600-18596400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:18576800-18594400	Weak transcription	Brain Anterior Caudate	brain
37	chr11:18576800-18599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:18577400-18599200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:18577600-18591400	Weak transcription	HSMMtube	muscle
40	chr11:18578000-18600600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
43	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
44	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
46	chr11:18579400-18595000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:18579600-18600800	Weak transcription	Colonic Mucosa	Colon
48	chr11:18580000-18587800	Weak transcription	Fetal Kidney	kidney
49	chr11:18580000-18590800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:18580000-18591000	Weak transcription	HUVEC	blood vessel

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