Variant report

Variant	rs4623881
Chromosome Location	chr11:18574099-18574100
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	chr11:18572038..18574109-chr11:18607520..18610133,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10500836	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10741747	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766483	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10766484	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10766485	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832940	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024690	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024699	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024711	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12224694	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12225037	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419063	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12574808	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577346	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395319	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395320	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34457574	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3925781	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4298881	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756949	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756950	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756952	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486434	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105889	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931630	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7934817	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7951508	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952284	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868069	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv975324	chr11:18563800-18581423	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4623881	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs4623881	LDHC	cis	Thyroid	GTEx
rs4623881	TSG101	cis	multi-tissue	Pritchard
rs4623881	TSG101	cis	Muscle Skeletal	GTEx
rs4623881	TSG101	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549000-18576400	Weak transcription	Gastric	stomach
2	chr11:18549000-18577000	Weak transcription	Spleen	Spleen
3	chr11:18549200-18577000	Weak transcription	Esophagus	oesophagus
4	chr11:18549200-18583400	Weak transcription	Small Intestine	intestine
5	chr11:18549200-18591400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:18549400-18576000	Weak transcription	Ovary	ovary
7	chr11:18549400-18576400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr11:18549400-18577000	Weak transcription	Colonic Mucosa	Colon
9	chr11:18549400-18579200	Weak transcription	Pancreas	Pancrea
10	chr11:18549400-18583400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:18549600-18575000	Weak transcription	Fetal Brain Female	brain
13	chr11:18549600-18575200	Weak transcription	Fetal Kidney	kidney
14	chr11:18549600-18576400	Weak transcription	Brain Substantia Nigra	brain
15	chr11:18549600-18576600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:18549600-18576800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:18549600-18577200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:18549600-18577800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
20	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
22	chr11:18549800-18575000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr11:18549800-18576200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:18549800-18576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:18549800-18577000	Weak transcription	Primary T cells from cord blood	blood
26	chr11:18549800-18582400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:18549800-18588200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:18549800-18592000	Weak transcription	NHLF	lung
29	chr11:18549800-18594400	Weak transcription	K562	blood
30	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:18550400-18575200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:18550600-18591400	Weak transcription	Dnd41	blood
33	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:18554000-18576000	Weak transcription	Brain Angular Gyrus	brain
35	chr11:18555800-18576400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:18555800-18582800	Weak transcription	NHEK	skin
37	chr11:18557800-18576600	Weak transcription	Psoas Muscle	Psoas
38	chr11:18558400-18576200	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:18558400-18592200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr11:18559200-18592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:18560600-18576200	Weak transcription	Brain Anterior Caudate	brain
42	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
43	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:18564000-18586400	Weak transcription	GM12878-XiMat	blood
46	chr11:18564200-18576200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:18566000-18576200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:18566200-18576000	Weak transcription	Right Ventricle	heart
50	chr11:18566200-18576800	Weak transcription	Brain Germinal Matrix	brain

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