Variant report

Variant	rs9633899
Chromosome Location	chr11:18546644-18546645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18546372..18549758-chr11:18653531..18658575,7	K562	blood:
2	chr11:18530137..18532670-chr11:18545448..18547562,2	K562	blood:
3	chr11:18546581..18551368-chr11:18654825..18657467,6	K562	blood:
4	chr11:18430626..18432747-chr11:18545645..18547445,2	K562	blood:
5	chr11:18546303..18549278-chr11:18609985..18612598,2	K562	blood:
6	chr11:18533507..18535848-chr11:18546408..18548301,3	K562	blood:
7	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151116	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000256588	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10219166	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832942	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832943	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10832945	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024670	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024674	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024675	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024676	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024678	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024683	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024685	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024689	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024706	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024716	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024723	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024724	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049851	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049909	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049912	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12222210	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12223858	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12223887	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12225461	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12225463	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12290527	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12418726	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419360	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12420702	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12420882	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12421881	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574333	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12575390	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12577874	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12803251	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16914838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16935504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271080	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279900	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305166	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28607050	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3781639	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55964013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55999230	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56097703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56151250	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56151849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56411332	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59032896	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61882885	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882887	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882903	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61882904	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61884677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7108487	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7109314	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130163	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72871737	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72876745	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950602	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9633899	TSG101	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
4	chr11:18523800-18547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:18524200-18547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:18524200-18547400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:18527200-18547200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:18532800-18547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:18533400-18547200	Weak transcription	A549	lung
10	chr11:18534800-18547200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:18535400-18547800	Weak transcription	Esophagus	oesophagus
12	chr11:18535600-18547600	Weak transcription	Aorta	Aorta
13	chr11:18535800-18547200	Weak transcription	HUVEC	blood vessel
14	chr11:18535800-18547400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:18535800-18547800	Weak transcription	Lung	lung
16	chr11:18536200-18547200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:18536200-18547200	Weak transcription	HSMMtube	muscle
18	chr11:18536600-18547200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:18536800-18547400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:18537200-18546800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:18537200-18547400	Weak transcription	Colonic Mucosa	Colon
22	chr11:18537400-18547200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:18537400-18547200	Weak transcription	Brain Angular Gyrus	brain
24	chr11:18537400-18547200	Weak transcription	Brain Substantia Nigra	brain
25	chr11:18537400-18547200	Weak transcription	NHLF	lung
26	chr11:18537400-18547400	Weak transcription	Brain Anterior Caudate	brain
27	chr11:18537400-18547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:18537600-18546800	Weak transcription	Fetal Brain Male	brain
29	chr11:18537800-18547200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:18537800-18547200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:18537800-18547400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:18537800-18547400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:18538000-18547200	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:18538800-18547200	Weak transcription	Fetal Stomach	stomach
35	chr11:18539400-18546800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:18539800-18546800	Weak transcription	NHDF-Ad	bronchial
37	chr11:18540000-18547000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:18540000-18547200	Weak transcription	Fetal Kidney	kidney
39	chr11:18540200-18547200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:18540400-18546800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:18540400-18547200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:18540400-18547400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr11:18540600-18547200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:18540800-18547200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:18540800-18547200	Weak transcription	Fetal Brain Female	brain
46	chr11:18541200-18547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:18542600-18546800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:18543400-18547000	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr11:18543600-18546800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:18543600-18547000	Genic enhancers	Primary T cells from cord blood	blood

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