Variant report

Variant	rs11070770
Chromosome Location	chr15:50654075-50654076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50651977-50656135	K562	blood:	n/a	n/a
2	POLR2A	chr15:50653768-50654263	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:50652123-50656758	MCF10A-Er-Src	breast:	n/a	n/a
4	SPI1	chr15:50653885-50654239	HL-60	blood:	n/a	n/a
5	POLR2A	chr15:50653775-50654256	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:50652108-50656068	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:50653827-50654367	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr15:50654069-50654184	A549	lung:	n/a	n/a
9	POLR2A	chr15:50653800-50654255	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:50653942-50654657	U87	brain:	n/a	n/a
11	POLR2A	chr15:50654014-50654273	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:50653582-50654331	SK-N-MC	brain:	n/a	n/a
13	MAX	chr15:50653977-50654236	NB4	blood:	n/a	chr15:50654094-50654104
14	POLR2A	chr15:50653806-50654330	HL-60	blood:	n/a	n/a
15	POLR2A	chr15:50653830-50654236	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr15:50653924-50654094	A549	lung:	n/a	n/a
17	POLR2A	chr15:50653513-50654353	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr15:50653637-50654266	MCF-7	breast:	n/a	n/a
19	POLR2A	chr15:50653893-50654239	HL-60	blood:	n/a	n/a
20	POLR2A	chr15:50653583-50654553	A549	lung:	n/a	n/a
21	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr15:50653468-50655954	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr15:50653542-50654383	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr15:50653700-50654608	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:50653801-50654282	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:50653224..50655834-chr15:50679603..50681544,2	MCF-7	breast:
2	chr15:50650545..50654228-chr15:50976566..50979826,3	MCF-7	breast:
3	chr15:50652761..50655517-chr15:50682002..50683698,2	MCF-7	breast:
4	chr15:50654014..50656203-chr15:50714863..50719215,3	K562	blood:
5	chr1:119682098..119684548-chr15:50651200..50654157,2	MCF-7	breast:
6	chr1:149222464..149224634-chr15:50652467..50655317,2	MCF-7	breast:
7	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
8	chr15:50652084..50654939-chr15:50731022..50732692,2	MCF-7	breast:
9	chr15:50653739..50656300-chr15:50709465..50712188,2	MCF-7	breast:
10	chr15:50653724..50655315-chr15:50681569..50683481,2	K562	blood:
11	chr15:50653824..50655842-chr15:50714990..50716546,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259715	TF binding region
ENSG00000231365	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000259465	Chromatin interaction
ENSG00000116874	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1056681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857071	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440601	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903381	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909202	1.00[ASN][1000 genomes]
rs12917303	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509458	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598020	1.00[ASN][1000 genomes]
rs2013885	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013888	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2033114	1.00[ASN][1000 genomes]
rs2414049	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450641	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45508400	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504781	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022563	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022564	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022565	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022567	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022569	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022570	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493426	1.00[ASN][1000 genomes]
rs6493439	0.80[EUR][1000 genomes]
rs677143	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71424053	0.82[EUR][1000 genomes]
rs72738935	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72738949	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8034849	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920021	1.00[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs11070770	GABPB1-AS1	cis	lung	GTEx
rs11070770	CTD-3110H11.1	cis	lung	GTEx
rs11070770	GABPB1-AS1	cis	Whole Blood	GTEx
rs11070770	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs11070770	CTD-3110H11.1	cis	Stomach	GTEx
rs11070770	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs11070770	GABPB1-AS1	cis	Artery Aorta	GTEx
rs11070770	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs11070770	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11070770	GABPB1-AS1	cis	Artery Tibial	GTEx
rs11070770	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs11070770	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs11070770	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs11070770	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs11070770	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11070770	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs11070770	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs11070770	GABPB1-AS1	cis	Stomach	GTEx
rs11070770	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs11070770	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs11070770	GABPB1-AS1	cis	Thyroid	GTEx
rs11070770	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs11070770	CTD-3110H11.1	cis	Thyroid	GTEx
rs11070770	GABPB2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50648200-50657200	Weak transcription	Esophagus	oesophagus
3	chr15:50648200-50658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:50648200-50664400	Weak transcription	Lung	lung
5	chr15:50648400-50660400	Weak transcription	Aorta	Aorta
6	chr15:50648800-50655600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:50649000-50658600	Weak transcription	Right Atrium	heart
8	chr15:50649200-50656400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
10	chr15:50649400-50654800	Weak transcription	Brain Germinal Matrix	brain
11	chr15:50649400-50655800	Strong transcription	HSMM	muscle
12	chr15:50649400-50656600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:50649400-50657800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:50649400-50659200	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:50649400-50664000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:50649600-50654600	Strong transcription	Osteobl	bone
17	chr15:50649600-50654800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr15:50649600-50654800	Weak transcription	Brain Substantia Nigra	brain
19	chr15:50649600-50655600	Weak transcription	Gastric	stomach
20	chr15:50649600-50656600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:50649600-50656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:50649600-50657400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:50649600-50660600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:50649600-50661800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:50649800-50654600	Strong transcription	Fetal Lung	lung
26	chr15:50649800-50655600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:50649800-50656600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:50649800-50664200	Weak transcription	Small Intestine	intestine
29	chr15:50649800-50664600	Weak transcription	Psoas Muscle	Psoas
30	chr15:50650000-50654200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:50650000-50656400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr15:50650000-50658000	Weak transcription	Fetal Heart	heart
33	chr15:50650000-50663000	Weak transcription	Fetal Brain Male	brain
34	chr15:50650000-50663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:50650200-50654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:50650200-50654600	Strong transcription	K562	blood
37	chr15:50650200-50655400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:50650200-50658200	Strong transcription	NHEK	skin
39	chr15:50650200-50662600	Weak transcription	NH-A	brain
40	chr15:50650200-50664000	Weak transcription	Spleen	Spleen
41	chr15:50650800-50655200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:50650800-50656000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:50650800-50659400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:50651000-50654400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:50651000-50654800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr15:50651000-50655600	Strong transcription	Fetal Intestine Large	intestine
47	chr15:50651200-50654400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:50651200-50655400	Strong transcription	GM12878-XiMat	blood
49	chr15:50651200-50656600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:50651400-50655400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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