Variant report

Variant	rs1052566
Chromosome Location	chr11:66105194-66105195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:66102626-66105682	SK-N-SH	brain:	n/a	chr11:66104331-66104346 chr11:66104355-66104370 chr11:66104353-66104368
2	POLR2A	chr11:66101875-66105316	IMR90	lung:	n/a	n/a
3	POLR2A	chr11:66104901-66105435	U87	brain:	n/a	n/a
4	POLR2A	chr11:66104861-66105507	GM12878	blood:	n/a	n/a
5	ELF1	chr11:66104929-66105383	GM12878	blood:	n/a	n/a
6	EP300	chr11:66104801-66105335	SK-N-SH_RA	brain:	n/a	n/a
7	CHD1	chr11:66102182-66106109	IMR90	lung:	n/a	n/a
8	JUND	chr11:66103106-66105677	SK-N-SH	brain:	n/a	chr11:66104295-66104302 chr11:66104294-66104303 chr11:66104295-66104303 chr11:66104293-66104305 chr11:66104294-66104304 chr11:66104293-66104304
9	TCF12	chr11:66103637-66105470	SK-N-SH	brain:	n/a	n/a
10	MAZ	chr11:66102235-66106377	IMR90	lung:	n/a	chr11:66104147-66104162 chr11:66104331-66104340 chr11:66104151-66104160 chr11:66104359-66104368 chr11:66106166-66106175 chr11:66106165-66106176 chr11:66104355-66104364 chr11:66104294-66104303 chr11:66104295-66104304
11	RCOR1	chr11:66102436-66106057	IMR90	lung:	n/a	n/a
12	EP300	chr11:66103534-66105272	SK-N-SH	brain:	n/a	chr11:66104295-66104304 chr11:66104294-66104303
13	RAD21	chr11:66102956-66105643	SK-N-SH	brain:	n/a	chr11:66104271-66104290 chr11:66104451-66104463
14	MXI1	chr11:66102620-66105695	IMR90	lung:	n/a	chr11:66104331-66104346 chr11:66104355-66104370 chr11:66104353-66104368

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:66105148-66105198	AG09319	gingival:	n/a
2	chr11:66105148-66105198	NB4	blood:	n/a
3	chr11:66105148-66105198	A549	lung:	n/a
4	chr11:66105148-66105198	GM12891	blood:	n/a
5	chr11:66105148-66105198	BJ	skin:	n/a
6	chr11:66105148-66105198	HNPCEpiC	eye:	n/a
7	chr11:66105148-66105198	T-47D	breast:	n/a
8	chr11:66105148-66105198	MCF10A-Er-Src	breast:	n/a
9	chr11:66105148-66105198	K562	blood:	n/a
10	chr11:66105148-66105198	GM06990	blood:	n/a
11	chr11:66105148-66105198	ProgFib	skin:	n/a
12	chr11:66105148-66105198	NHBE	bronchial:	n/a
13	chr11:66105148-66105198	Caco-2	colon:	n/a
14	chr11:66105148-66105198	HRCEpiC	kidney:	n/a
15	chr11:66105148-66105198	RPTEC	kidney:	n/a
16	chr11:66105148-66105198	GM12878	blood:	n/a
17	chr11:66105148-66105198	NHDF-neo	bronchial:	n/a
18	chr11:66105148-66105198	GM19239	blood:	n/a
19	chr11:66105148-66105198	PrEC	prostate:	n/a
20	chr11:66105148-66105198	LNCaP	prostate:	n/a
21	chr11:66105148-66105198	HUVEC	blood vessel:	n/a
22	chr11:66105148-66105198	AG10803	skin:	n/a
23	chr11:66105148-66105198	HCT-116	colon:	n/a
24	chr11:66105148-66105198	SK-N-MC	brain:	n/a
25	chr11:66105148-66105198	H1-hESC	embryonic stem cell:	embryo
26	chr11:66105148-66105198	HRPEpiC	eye:	n/a
27	chr11:66105148-66105198	SK-N-SH_RA	brain:	n/a
28	chr11:66105148-66105198	ECC-1	luminal epithelium:	n/a
29	chr11:66105148-66105198	HL-60	blood:	n/a
30	chr11:66105148-66105198	SKMC	muscle:	n/a
31	chr11:66105148-66105198	HCPEpiC	choroid plexus:	n/a
32	chr11:66105148-66105198	HRE	kidney:	n/a
33	chr11:66105148-66105198	NT2-D1	testis:	n/a
34	chr11:66105148-66105198	GM12892	blood:	n/a
35	chr11:66105148-66105198	HEK293	kidney:	embryo
36	chr11:66105148-66105198	HepG2	liver:	n/a
37	chr11:66105148-66105198	ovcar-3	ovarian:	n/a
38	chr11:66105148-66105198	HCM	heart:	n/a
39	chr11:66105148-66105198	SAEC	small airway:	n/a
40	chr11:66105148-66105198	CMK	blood:	n/a
41	chr11:66105148-66105198	MCF-7	breast:	n/a
42	chr11:66105148-66105198	U87	brain:	n/a
43	chr11:66105148-66105198	AG04450	lung:	fetal
44	chr11:66105148-66105198	NH-A	brain:	n/a
45	chr11:66105148-66105198	AoSMC	blood vessel:	n/a
46	chr11:66105148-66105198	Hepatocyte	liver:	n/a
47	chr11:66105148-66105198	IMR90	lung:	fetal
48	chr11:66105148-66105198	HIPEpiC	eye:	n/a
49	chr11:66105148-66105198	HMEC	breast:	n/a
50	chr11:66105148-66105198	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66055819..66057691-chr11:66103911..66105498,2	K562	blood:
2	chr11:66052249..66054204-chr11:66103456..66106375,2	K562	blood:
3	chr11:66077376..66081785-chr11:66101114..66107038,7	MCF-7	breast:
4	chr11:66053447..66056540-chr11:66100445..66105768,7	MCF-7	breast:
5	chr11:66102581..66106910-chr11:66137391..66141246,5	MCF-7	breast:
6	chr11:66103854..66118324-chr11:66119048..66141728,55	K562	blood:
7	chr11:66055597..66057691-chr11:66102656..66105498,2	K562	blood:

Variant related genes	Relation type
RIN1	TF binding region
RIN1	CpG island
ENSG00000174851	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000174669	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2276106	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs35936931	0.80[EUR][1000 genomes]
rs4930355	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66733929	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs68162171	0.84[EUR][1000 genomes]
rs72938583	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv897781	chr11:66095967-66116911	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv1813137	chr11:66098322-66106725	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
9	nsv897782	chr11:66099222-66116911	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	esv1850142	chr11:66099494-66105817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1052566	ACTN3	cis	Muscle Skeletal	GTEx
rs1052566	CTD-3074O7.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66098400-66108800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:66103400-66106200	Enhancers	Fetal Brain Male	brain
3	chr11:66103600-66106200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:66103600-66107600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:66103800-66106200	Weak transcription	Aorta	Aorta
6	chr11:66104000-66106000	Weak transcription	Small Intestine	intestine
7	chr11:66104200-66105200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr11:66104200-66105200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:66104200-66105200	Genic enhancers	Fetal Stomach	stomach
10	chr11:66104200-66105200	Genic enhancers	Pancreas	Pancrea
11	chr11:66104200-66105200	Genic enhancers	Thymus	Thymus
12	chr11:66104200-66105400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:66104200-66105400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr11:66104200-66105400	Genic enhancers	Spleen	Spleen
15	chr11:66104200-66105400	Enhancers	HUVEC	blood vessel
16	chr11:66104200-66106000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr11:66104200-66106200	Enhancers	HSMMtube	muscle
18	chr11:66104200-66106600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:66104200-66107800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:66104200-66109000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:66104400-66105200	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr11:66104400-66105200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:66104400-66105200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr11:66104400-66105200	Genic enhancers	Rectal Mucosa Donor 29	rectum
25	chr11:66104400-66105400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:66104400-66105600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:66104400-66105600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr11:66104400-66105600	Enhancers	A549	lung
29	chr11:66104400-66105800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:66104400-66106000	Genic enhancers	Fetal Muscle Leg	muscle
31	chr11:66104400-66106200	Weak transcription	Primary B cells from cord blood	blood
32	chr11:66104400-66106200	Weak transcription	K562	blood
33	chr11:66104400-66106600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:66104400-66106800	Genic enhancers	NHLF	lung
35	chr11:66104400-66107000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:66104400-66107200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr11:66104400-66107800	Enhancers	HMEC	breast
38	chr11:66104400-66110400	Strong transcription	Dnd41	blood
39	chr11:66104600-66105200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:66104600-66105200	Genic enhancers	Fetal Thymus	thymus
41	chr11:66104600-66105200	Enhancers	Hela-S3	cervix
42	chr11:66104600-66105200	Transcr. at gene 5' and 3'	NHEK	skin
43	chr11:66104600-66105400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:66104600-66105400	Genic enhancers	Brain Inferior Temporal Lobe	brain
45	chr11:66104600-66105600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr11:66104600-66105600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr11:66104600-66105800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:66104600-66105800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:66104600-66106000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:66104600-66106000	Weak transcription	Ovary	ovary

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