Variant report

Variant	rs2305166
Chromosome Location	chr11:18591645-18591646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10219166	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10500835	0.90[TSI][hapmap]
rs10832938	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832942	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832943	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024670	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11024671	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024674	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024675	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024677	0.85[TSI][hapmap]
rs11024678	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024679	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024683	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024685	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024688	0.85[TSI][hapmap]
rs11024689	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024695	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024696	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024706	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024723	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024724	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024727	0.81[TSI][hapmap]
rs12049851	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12049909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12049912	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12222154	0.90[TSI][hapmap]
rs12222210	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12223858	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12223887	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12225461	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12225463	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12289223	0.90[TSI][hapmap]
rs12290527	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12418726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12419360	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12419592	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12420702	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420882	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12574333	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12575390	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12577874	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12803251	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16914838	0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16935504	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16935575	0.90[TSI][hapmap]
rs2271080	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279900	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279902	0.85[TSI][hapmap]
rs28607050	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781639	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781640	0.85[TSI][hapmap]
rs4436523	0.85[TSI][hapmap]
rs4757673	0.95[JPT][hapmap]
rs55964013	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55999230	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56097703	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56151250	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56151849	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56411332	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59032896	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61882885	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61882887	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61882903	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61882904	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61884677	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7108487	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7109314	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7109496	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs7130163	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72871737	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72876745	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950602	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9633899	0.90[AMR][1000 genomes];0.90[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2305166	TSG101	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
3	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
5	chr11:18549800-18592000	Weak transcription	NHLF	lung
6	chr11:18549800-18594400	Weak transcription	K562	blood
7	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:18558400-18592200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:18559200-18592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
12	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr11:18567200-18594600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
18	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:18574600-18592200	Strong transcription	Liver	Liver
22	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:18576600-18596400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:18576800-18594400	Weak transcription	Brain Anterior Caudate	brain
26	chr11:18576800-18599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:18577400-18599200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:18578000-18600600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
31	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
32	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
34	chr11:18579400-18595000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:18579600-18600800	Weak transcription	Colonic Mucosa	Colon
36	chr11:18580000-18595400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr11:18580000-18595400	Weak transcription	NH-A	brain
38	chr11:18580000-18596400	Weak transcription	HepG2	liver
39	chr11:18580000-18608600	Weak transcription	Hela-S3	cervix
40	chr11:18580200-18608600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:18581000-18609000	Weak transcription	Pancreas	Pancrea
42	chr11:18581400-18595400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:18582600-18591800	Weak transcription	Brain Angular Gyrus	brain
44	chr11:18582600-18600600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:18583000-18591800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr11:18583000-18592600	Weak transcription	Aorta	Aorta
47	chr11:18583000-18592800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:18583000-18608200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:18583000-18609400	Weak transcription	Esophagus	oesophagus
50	chr11:18583200-18592800	Weak transcription	Rectal Smooth Muscle	rectum

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