Variant report

Variant	rs5998368
Chromosome Location	chr22:32677130-32677131
allele	A/G
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	MYC	chr22:32677068-32677481	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr22:32677102-32677512	MCF10A-Er-Src	breast:	n/a	chr22:32677357-32677369
3	TEAD4	chr22:32677086-32677449	ECC-1	luminal epithelium:	n/a	n/a
4	FOS	chr22:32677064-32677402	MCF10A-Er-Src	breast:	n/a	n/a
5	TEAD4	chr22:32677097-32677427	ECC-1	luminal epithelium:	n/a	n/a
6	NR3C1	chr22:32677068-32677350	ECC-1	luminal epithelium:	n/a	chr22:32677278-32677292
7	NR3C1	chr22:32677117-32677380	ECC-1	luminal epithelium:	n/a	chr22:32677278-32677292
8	FOS	chr22:32677066-32677422	MCF10A-Er-Src	breast:	n/a	n/a
9	NFIC	chr22:32677046-32677499	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr22:32677092-32677543	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr22:32676991-32677450	ECC-1	luminal epithelium:	n/a	n/a
12	FOS	chr22:32677071-32677438	MCF10A-Er-Src	breast:	n/a	n/a
13	NR3C1	chr22:32677000-32677565	A549	lung:	n/a	chr22:32677278-32677292
14	FOS	chr22:32677074-32677421	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr22:32677055-32677480	MCF10A-Er-Src	breast:	n/a	n/a
16	MAX	chr22:32677088-32677536	ECC-1	luminal epithelium:	n/a	n/a
17	NR3C1	chr22:32677105-32677466	A549	lung:	n/a	chr22:32677278-32677292
18	STAT3	chr22:32677072-32677512	MCF10A-Er-Src	breast:	n/a	chr22:32677357-32677369

Variant related genes	Relation type
ENSG00000273325	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11703318	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703608	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703659	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687156	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994522	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994535	0.81[EUR][1000 genomes]
rs5998390	1.00[ASN][1000 genomes]
rs5998392	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396997	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135855	0.84[AFR][1000 genomes]
rs8138166	0.83[EUR][1000 genomes]
rs8142833	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv834178	chr22:32490449-32677521	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	esv2753006	chr22:32592120-32719481	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv979756	chr22:32669633-32681470	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5998368	RP1-149A16.12	cis	Thyroid	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32674000-32690000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr22:32676200-32677800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr22:32676400-32677200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
4	chr22:32676400-32677400	Enhancers	Brain Cingulate Gyrus	brain
5	chr22:32676400-32677600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:32676400-32677800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:32676400-32677800	Enhancers	HMEC	breast
8	chr22:32676800-32677200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:32676800-32677200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:32676800-32677400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:32676800-32677400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:32676800-32677400	Enhancers	Brain Germinal Matrix	brain
13	chr22:32676800-32677400	Enhancers	NH-A	brain
14	chr22:32677000-32677200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr22:32677000-32677400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr22:32677000-32677400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr22:32677000-32677400	Enhancers	Brain Anterior Caudate	brain
18	chr22:32677000-32677400	Active TSS	Brain Hippocampus Middle	brain
19	chr22:32677000-32677400	Enhancers	Brain Substantia Nigra	brain
20	chr22:32677000-32677400	Enhancers	Fetal Brain Male	brain
21	chr22:32677000-32677600	Active TSS	Fetal Brain Female	brain
22	chr22:32677000-32677800	Enhancers	NHEK	skin
23	chr22:32677000-32680400	Weak transcription	Brain Angular Gyrus	brain

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