Variant report

Variant	rs9404059
Chromosome Location	chr6:101331497-101331498
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	CEBPB	chr6:101331250-101331545	Hela-S3	cervix:	n/a	chr6:101331407-101331418
2	CEBPB	chr6:101330567-101331603	K562	blood:	n/a	chr6:101331407-101331418
3	CEBPB	chr6:101331224-101331609	A549	lung:	n/a	chr6:101331407-101331418
4	CEBPB	chr6:101331231-101331595	IMR90	lung:	n/a	chr6:101331407-101331418
5	CEBPB	chr6:101331220-101331613	MCF-7	breast:	n/a	chr6:101331407-101331418
6	CEBPB	chr6:101331226-101331588	H1-hESC	embryonic stem cell:	n/a	chr6:101331407-101331418
7	CEBPB	chr6:101331227-101331603	HepG2	liver:	n/a	chr6:101331407-101331418

No.	Distal block	Cell Line	Cell type
1	chr6:101162432..101165009-chr6:101330194..101333113,2	K562	blood:
2	chr6:101328677..101332841-chr6:101334376..101338552,5	K562	blood:
3	chr6:101327650..101330005-chr6:101331234..101332758,2	K562	blood:

Variant related genes	Relation type
ASCC3	TF binding region
ENSG00000112249	Chromatin interaction
ENSG00000260000	Chromatin interaction
ENSG00000270987	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11155708	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11755579	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11758174	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209186	0.96[ASN][1000 genomes]
rs13193416	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13205402	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13212730	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13220881	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17672397	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1813223	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004276	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2398247	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34555037	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34716527	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4464803	0.81[ASN][1000 genomes]
rs4840157	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4840159	0.81[EUR][1000 genomes]
rs4840160	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840164	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs599934	0.81[ASN][1000 genomes]
rs62420689	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62422111	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs669543	0.84[ASN][1000 genomes]
rs6917195	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694418	0.84[ASN][1000 genomes]
rs7453078	0.81[ASN][1000 genomes]
rs7758630	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9322270	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322271	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9322276	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322279	0.85[AMR][1000 genomes]
rs9377236	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377240	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377241	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386258	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390698	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390702	0.85[AMR][1000 genomes]
rs9399695	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399697	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404060	0.88[ASN][1000 genomes]
rs979122	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791225	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9404059	ASCC3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101329800-101331600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:101329800-101333000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:101329800-101335000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:101329800-101340600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:101330000-101332600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:101330200-101331600	Weak transcription	Primary B cells from cord blood	blood
7	chr6:101330200-101331800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:101330200-101333000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:101330200-101340000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:101330400-101331600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:101330400-101339000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:101330600-101333800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:101330600-101334000	Weak transcription	NH-A	brain
14	chr6:101330600-101335000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:101330800-101339000	Weak transcription	K562	blood
16	chr6:101331000-101331600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:101331000-101331600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:101331200-101331600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr6:101331400-101331600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:101331400-101331600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:101331400-101331600	Enhancers	Placenta	Placenta
22	chr6:101331400-101333000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:101331400-101333200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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