Variant report

Variant	rs1546358
Chromosome Location	chr11:66175261-66175262
allele	C/G/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	CTCF	chr11:66175260-66175410	GM06990	blood:	n/a	n/a
2	POLR2A	chr11:66174950-66175459	K562	blood:	n/a	n/a
3	CTCF	chr11:66175204-66176687	HCT-116	colon:	n/a	chr11:66176031-66176049 chr11:66176099-66176117 chr11:66176100-66176116 chr11:66176033-66176054 chr11:66176032-66176048 chr11:66176102-66176115
4	MYC	chr11:66175232-66175409	K562	blood:	n/a	n/a
5	CTCF	chr11:66175200-66175350	GM12864	blood:	n/a	n/a
6	JUND	chr11:66175257-66175419	K562	blood:	n/a	n/a
7	CEBPD	chr11:66175109-66175525	K562	blood:	n/a	n/a
8	RCOR1	chr11:66175151-66175519	K562	blood:	n/a	n/a
9	RCOR1	chr11:66175225-66175456	K562	blood:	n/a	n/a
10	TAL1	chr11:66175165-66175530	K562	blood:	n/a	n/a
11	GATA1	chr11:66174954-66175480	K562	blood:	n/a	chr11:66175050-66175058
12	EP300	chr11:66175195-66175411	K562	blood:	n/a	n/a
13	ARID3A	chr11:66175246-66175427	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66174951..66176605-chr11:66445089..66446742,2	K562	blood:
2	chr11:66174002..66176037-chr11:66244624..66246480,2	MCF-7	breast:
3	chr11:66171206..66173547-chr11:66174703..66176452,2	MCF-7	breast:
4	chr11:66174529..66176605-chr11:66189846..66192239,2	K562	blood:
5	chr11:66173458..66175386-chr11:66246619..66249272,2	MCF-7	breast:
6	chr11:66175166..66176626-chr11:66445371..66446673,13	K562	blood:
7	chr11:66173655..66176306-chr11:66183166..66186139,2	K562	blood:
8	chr11:66174524..66177610-chr11:66443614..66447044,3	K562	blood:

Variant related genes	Relation type
ENSG00000254510	TF binding region
ENSG00000255517	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000254986	Chromatin interaction
ENSG00000174576	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1039594	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1047029	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10750784	0.87[EUR][1000 genomes]
rs10791869	0.89[EUR][1000 genomes]
rs10791872	0.92[EUR][1000 genomes]
rs10791874	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10791876	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10896111	0.87[EUR][1000 genomes]
rs10896112	0.88[EUR][1000 genomes]
rs10896115	0.88[EUR][1000 genomes]
rs10896116	0.92[EUR][1000 genomes]
rs11227465	0.88[EUR][1000 genomes]
rs11601396	0.88[EUR][1000 genomes]
rs12416747	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12576299	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12577196	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12785321	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12785651	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12786563	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12794121	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1785633	0.85[EUR][1000 genomes]
rs1785639	0.82[EUR][1000 genomes]
rs1892940	0.89[EUR][1000 genomes]
rs2236679	0.84[EUR][1000 genomes]
rs2279861	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2279862	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2282530	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3016767	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3177514	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34043951	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4244813	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4466842	0.81[AMR][1000 genomes]
rs4930177	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4930178	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4930179	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930181	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4930360	0.85[EUR][1000 genomes]
rs4930362	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930363	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4930366	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930368	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55998145	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56123976	0.89[EUR][1000 genomes]
rs56321771	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61891449	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6591213	0.94[EUR][1000 genomes]
rs6591215	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6591217	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66810040	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7104253	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7104570	1.00[EUR][1000 genomes]
rs7105015	0.98[EUR][1000 genomes]
rs7105401	0.99[EUR][1000 genomes]
rs7107191	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7110944	0.87[EUR][1000 genomes]
rs7117630	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7126018	0.91[EUR][1000 genomes]
rs73489638	0.88[EUR][1000 genomes]
rs7938676	0.96[EUR][1000 genomes]
rs7939111	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7940980	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs905770	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs947978	0.85[EUR][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	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	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
3	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
4	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
5	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
6	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1546358	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs1546358	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66173600-66176000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:66173600-66176400	Weak transcription	Spleen	Spleen
3	chr11:66174200-66175800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:66175000-66175800	Enhancers	K562	blood
5	chr11:66175200-66175800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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