Variant report

Variant	rs1945302
Chromosome Location	chr11:66337498-66337499
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	POLR2A	chr11:66337436-66338802	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66334662..66337726-chr11:66444588..66447609,3	K562	blood:
2	chr11:66311475..66316022-chr11:66335981..66338223,4	MCF-7	breast:

Variant related genes	Relation type
CTSF	TF binding region
ENSG00000173914	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000248746	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1044522	0.92[ASN][1000 genomes]
rs10896126	0.90[ASN][1000 genomes]
rs1201433	0.82[ASN][1000 genomes]
rs1791679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242663	1.00[ASN][1000 genomes]
rs2511224	0.86[ASN][1000 genomes]
rs4277117	0.88[ASN][1000 genomes]
rs4930383	0.95[ASN][1000 genomes]
rs4930384	0.99[ASN][1000 genomes]
rs544021	0.83[AFR][1000 genomes]
rs597626	0.83[AFR][1000 genomes]
rs607736	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610293	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7951189	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1945302	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs1945302	ACTN3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66330400-66337800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:66331400-66337800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:66331600-66337800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:66336000-66337600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:66336000-66337800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:66336200-66337600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:66336200-66338400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:66336400-66337600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:66336400-66337800	Weak transcription	HSMMtube	muscle
11	chr11:66336400-66338000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr11:66336400-66338000	Weak transcription	Fetal Kidney	kidney
13	chr11:66336400-66346600	Weak transcription	Right Atrium	heart
14	chr11:66336600-66337600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr11:66336600-66337600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr11:66336600-66337600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:66336800-66338800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr11:66336800-66338800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr11:66336800-66338800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr11:66337000-66337800	Weak transcription	Ovary	ovary
21	chr11:66337000-66338000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:66337000-66346600	Weak transcription	K562	blood
23	chr11:66337200-66337600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:66337200-66337600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:66337400-66338400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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