Variant report

Variant	rs11024699
Chromosome Location	chr11:18549566-18549567
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:18547452-18549568	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr11:18549007-18549648	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr11:18549377-18549796	MCF-7	breast:	n/a	n/a
4	POLR2A	chr11:18547906-18549610	K562	blood:	n/a	n/a
5	POLR2A	chr11:18547454-18549716	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr11:18547489-18549714	GM12891	blood:	n/a	n/a
7	POLR2A	chr11:18547491-18549640	Hela-S3	cervix:	n/a	n/a
8	PBX3	chr11:18548189-18549614	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr11:18549520-18549609	K562	blood:	n/a	n/a
10	POLR2A	chr11:18547789-18549635	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr11:18547434-18549791	IMR90	lung:	n/a	n/a
12	POLR2A	chr11:18547890-18549648	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:18547848-18549804	K562	blood:	n/a	n/a
14	FOS	chr11:18548050-18549684	HUVEC	blood vessel:	n/a	chr11:18548088-18548102
15	POLR2A	chr11:18547705-18549580	IMR90	lung:	n/a	n/a
16	ZNF274	chr11:18548853-18549775	K562	blood:	n/a	n/a
17	HCFC1	chr11:18547281-18549636	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr11:18547391-18549866	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr11:18549168-18549613	U87	brain:	n/a	n/a
20	SMARCC1	chr11:18547823-18549598	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18546372..18549758-chr11:18653531..18658575,7	K562	blood:
2	chr11:18546581..18551368-chr11:18654825..18657467,6	K562	blood:
3	chr11:18432193..18433875-chr11:18547475..18550164,2	MCF-7	breast:
4	chr11:18547238..18549661-chr11:18600782..18603302,3	MCF-7	breast:
5	chr11:18414795..18417618-chr11:18546727..18549809,4	MCF-7	breast:
6	chr11:18343253..18347316-chr11:18546908..18550670,5	K562	blood:
7	chr11:18415765..18417941-chr11:18547561..18549649,2	K562	blood:
8	chr11:18479966..18482806-chr11:18549124..18551467,2	K562	blood:
9	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:
10	chr11:18414231..18417142-chr11:18548434..18550099,2	K562	blood:
11	chr11:18415399..18418482-chr11:18547632..18550708,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LDHAL6A-1	chr11:18548579-18550760	NONHSAT018294

No data

Variant related genes	Relation type
TSG101	TF binding region
ENSG00000179119	Chromatin interaction
ENSG00000151116	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000110768	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10500836	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10741747	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10766483	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10766484	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766485	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832940	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024690	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024711	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12224694	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12225037	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12419063	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12574808	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12577346	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1395319	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1395320	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34457574	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3925781	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4298881	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4623881	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756949	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756950	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756952	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6486434	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7105889	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7107057	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7931630	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7934817	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7951508	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7952284	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs868069	0.88[AMR][1000 genomes];0.93[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	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	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11024699	TSG101	cis	Muscle Skeletal	GTEx
rs11024699	TSG101	cis	multi-tissue	Pritchard
rs11024699	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18547000-18549600	Active TSS	GM12878-XiMat	blood
2	chr11:18547200-18549600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:18547200-18549600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr11:18547200-18549600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:18547200-18549600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:18547200-18549600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:18547200-18549600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:18547200-18549600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:18547200-18549600	Active TSS	Fetal Intestine Large	intestine
10	chr11:18547200-18549600	Active TSS	K562	blood
11	chr11:18547200-18549800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:18547200-18549800	Active TSS	Psoas Muscle	Psoas
13	chr11:18547200-18549800	Active TSS	Stomach Smooth Muscle	stomach
14	chr11:18547400-18549600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:18547400-18549600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:18547400-18549600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr11:18547400-18549600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr11:18547400-18549600	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr11:18547400-18549600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:18547400-18549600	Active TSS	HSMMtube	muscle
21	chr11:18547400-18549800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:18547400-18549800	Active TSS	Right Ventricle	heart
23	chr11:18547400-18549800	Active TSS	A549	lung
24	chr11:18547600-18549600	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr11:18547600-18549600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:18547600-18549600	Active TSS	HSMM	muscle
27	chr11:18547600-18549600	Active TSS	NHDF-Ad	bronchial
28	chr11:18548600-18549600	Flanking Active TSS	HUVEC	blood vessel
29	chr11:18548600-18549800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:18548800-18549600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr11:18548800-18549600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr11:18548800-18549600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr11:18548800-18549600	Flanking Active TSS	Liver	Liver
34	chr11:18548800-18549600	Flanking Active TSS	Fetal Lung	lung
35	chr11:18548800-18549600	Flanking Active TSS	NH-A	brain
36	chr11:18548800-18549800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:18548800-18549800	Flanking Active TSS	Hela-S3	cervix
38	chr11:18549000-18549600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr11:18549000-18549600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:18549000-18549600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr11:18549000-18549600	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr11:18549000-18549600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr11:18549000-18549600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr11:18549000-18549600	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr11:18549000-18549600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr11:18549000-18549600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr11:18549000-18549600	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr11:18549000-18549600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr11:18549000-18549600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr11:18549000-18549600	Flanking Active TSS	Osteobl	bone

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