Variant report

Variant	rs10273320
Chromosome Location	chr7:66090736-66090737
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	STAT3	chr7:66090661-66090840	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66086058..66091828-chr7:66092043..66096410,8	K562	blood:
2	chr7:66086645..66090963-chr7:66091966..66094682,7	K562	blood:
3	chr7:66087482..66091666-chr7:66091713..66095048,5	MCF-7	breast:

Variant related genes	Relation type
KCTD7	TF binding region
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10224536	0.86[EUR][1000 genomes]
rs10225392	0.89[EUR][1000 genomes]
rs10226294	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10228381	0.85[EUR][1000 genomes]
rs10229580	0.89[EUR][1000 genomes]
rs10231860	0.83[EUR][1000 genomes]
rs10234747	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10235037	0.83[EUR][1000 genomes]
rs10237244	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10239200	0.83[EUR][1000 genomes]
rs10240153	0.89[EUR][1000 genomes]
rs10240582	0.89[EUR][1000 genomes]
rs10241395	0.84[EUR][1000 genomes]
rs10243608	0.84[EUR][1000 genomes]
rs10244459	0.84[EUR][1000 genomes]
rs10244602	0.84[EUR][1000 genomes]
rs10252133	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10255813	0.84[EUR][1000 genomes]
rs10256117	0.86[EUR][1000 genomes]
rs10257393	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10258628	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10262184	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265154	0.88[EUR][1000 genomes]
rs10266041	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10267834	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10270326	0.86[EUR][1000 genomes]
rs10271177	0.89[EUR][1000 genomes]
rs10273402	0.81[EUR][1000 genomes]
rs10277231	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10278343	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10278763	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10280431	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10280717	0.83[EUR][1000 genomes]
rs10281544	0.88[EUR][1000 genomes]
rs10281734	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10282310	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10282522	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10479728	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1064795	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12234826	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12333749	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12334214	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13437901	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13438432	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17138208	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17138274	0.89[EUR][1000 genomes]
rs1882656	0.88[EUR][1000 genomes]
rs1882657	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28368585	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28375318	0.87[EUR][1000 genomes]
rs28379824	0.81[EUR][1000 genomes]
rs28460006	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28474923	0.84[EUR][1000 genomes]
rs28526115	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28560293	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28607736	0.86[EUR][1000 genomes]
rs28615327	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28634091	0.81[EUR][1000 genomes]
rs28657758	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3757419	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3764904	0.88[EUR][1000 genomes]
rs3778907	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3800814	0.81[EUR][1000 genomes]
rs3814464	0.82[AFR][1000 genomes]
rs3823607	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3823609	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3962133	0.84[EUR][1000 genomes]
rs4518552	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718417	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57902746	0.88[EUR][1000 genomes]
rs59079543	0.88[EUR][1000 genomes]
rs60972148	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61093354	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61700307	0.88[EUR][1000 genomes]
rs6964080	0.88[EUR][1000 genomes]
rs6973897	0.89[EUR][1000 genomes]
rs6974601	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73133809	0.83[EUR][1000 genomes]
rs73133816	0.84[EUR][1000 genomes]
rs73133851	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133859	0.88[EUR][1000 genomes]
rs73133865	0.88[EUR][1000 genomes]
rs73135905	0.88[EUR][1000 genomes]
rs73135907	0.88[EUR][1000 genomes]
rs73135909	0.88[EUR][1000 genomes]
rs73135917	0.88[EUR][1000 genomes]
rs73135922	0.88[EUR][1000 genomes]
rs73135925	0.88[EUR][1000 genomes]
rs73135950	0.88[EUR][1000 genomes]
rs73135960	0.89[EUR][1000 genomes]
rs73135973	0.87[EUR][1000 genomes]
rs73137960	0.86[EUR][1000 genomes]
rs73137963	0.83[EUR][1000 genomes]
rs73139941	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73152708	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73152725	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9654843	0.88[EUR][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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10273320	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs10273320	GS1-124K5.12	cis	Artery Tibial	GTEx
rs10273320	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66085000-66090800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:66086800-66092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:66087600-66092200	Weak transcription	K562	blood
4	chr7:66087600-66092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:66089800-66092800	Enhancers	Placenta	Placenta
6	chr7:66090200-66091800	Enhancers	HepG2	liver
7	chr7:66090200-66092800	Weak transcription	Stomach Mucosa	stomach
8	chr7:66090400-66092200	Enhancers	NHDF-Ad	bronchial
9	chr7:66090400-66092800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:66090600-66090800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:66090600-66092200	Enhancers	Colon Smooth Muscle	Colon
12	chr7:66090600-66093000	Enhancers	NHLF	lung

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