Variant report

Variant	rs28473627
Chromosome Location	chr9:136996067-136996068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr9:136995951-136996566	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBL1XR1	chr9:136996062-136996250	K562	blood:	n/a	n/a
3	GTF2F1	chr9:136995913-136996650	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr9:136996023-136996509	H1-hESC	embryonic stem cell:	n/a	chr9:136996424-136996433
5	TEAD4	chr9:136996012-136996632	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:136995981-136996744	ECC-1	luminal epithelium:	n/a	n/a
7	SP1	chr9:136995980-136996598	H1-hESC	embryonic stem cell:	n/a	chr9:136996268-136996279
8	TEAD4	chr9:136996001-136996712	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr9:136996016-136996216	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr9:136995897-136996780	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr9:136996026-136996558	Hela-S3	cervix:	n/a	chr9:136996424-136996433
12	RCOR1	chr9:136996060-136996525	Hela-S3	cervix:	n/a	n/a
13	USF2	chr9:136996026-136996544	Hela-S3	cervix:	n/a	n/a
14	MAX	chr9:136996042-136996771	ECC-1	luminal epithelium:	n/a	n/a
15	RFX5	chr9:136995917-136996595	Hela-S3	cervix:	n/a	n/a
16	SMC3	chr9:136996007-136996530	Hela-S3	cervix:	n/a	chr9:136996421-136996435 chr9:136996242-136996249
17	CEBPB	chr9:136996059-136996574	Hela-S3	cervix:	n/a	n/a
18	SP1	chr9:136996008-136996534	H1-hESC	embryonic stem cell:	n/a	chr9:136996268-136996279
19	TEAD4	chr9:136996019-136996617	HepG2	liver:	n/a	n/a
20	MAFK	chr9:136996024-136996514	Hela-S3	cervix:	n/a	n/a
21	TEAD4	chr9:136996059-136996595	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr9:136996067-136996558	H1-hESC	embryonic stem cell:	n/a	n/a
23	TCF12	chr9:136995899-136996732	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr9:136996022-136996566	ECC-1	luminal epithelium:	n/a	n/a
25	MAZ	chr9:136996064-136996641	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr9:136996065-136997092	Hela-S3	cervix:	n/a	n/a
27	MAX	chr9:136995939-136996727	MCF-7	breast:	n/a	n/a
28	NFIC	chr9:136996009-136996708	ECC-1	luminal epithelium:	n/a	n/a
29	CHD2	chr9:136996007-136996659	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZKSCAN1	chr9:136995788-136996687	Hela-S3	cervix:	n/a	n/a
31	MAX	chr9:136995985-136996627	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr9:136995963-136996722	Hela-S3	cervix:	n/a	n/a
33	GABPA	chr9:136996031-136996760	MCF-7	breast:	n/a	chr9:136996392-136996406
34	MXI1	chr9:136995907-136996690	Hela-S3	cervix:	n/a	n/a
35	ZBTB7A	chr9:136995927-136996870	ECC-1	luminal epithelium:	n/a	n/a
36	MAX	chr9:136995987-136996608	ECC-1	luminal epithelium:	n/a	n/a
37	TCF12	chr9:136995947-136996833	ECC-1	luminal epithelium:	n/a	n/a
38	TEAD4	chr9:136995854-136996674	ECC-1	luminal epithelium:	n/a	n/a
39	ZBTB7A	chr9:136995972-136996618	ECC-1	luminal epithelium:	n/a	n/a
40	TCF7L2	chr9:136996017-136996605	Hela-S3	cervix:	n/a	chr9:136996123-136996130
41	TAF1	chr9:136996034-136996555	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136737938..136739664-chr9:136994862..136997731,2	MCF-7	breast:
2	chr9:136992413..136997235-chr9:136998349..137003411,7	K562	blood:
3	chr9:136994448..136996074-chr9:136999589..137002197,2	K562	blood:

No data

Variant related genes	Relation type
WDR5	TF binding region
ENSG00000273249	Chromatin interaction
ENSG00000196363	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28401669	0.81[ASN][1000 genomes]
rs28408860	0.99[ASN][1000 genomes]
rs28437234	0.96[ASN][1000 genomes]
rs28549934	0.82[ASN][1000 genomes]
rs28580780	0.99[ASN][1000 genomes]
rs28581991	0.86[ASN][1000 genomes]
rs28587783	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28602914	0.93[ASN][1000 genomes]
rs28616242	0.96[ASN][1000 genomes]
rs28759362	0.96[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	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136990800-136996200	Enhancers	Fetal Muscle Leg	muscle
2	chr9:136991000-136999400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:136992800-136996600	Enhancers	Fetal Muscle Trunk	muscle
4	chr9:136994400-136996200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:136994400-136996400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:136994400-136999400	Weak transcription	Primary B cells from cord blood	blood
7	chr9:136994600-136999200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:136994600-136999400	Weak transcription	Spleen	Spleen
9	chr9:136994600-136999800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:136994800-136996200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:136995000-136996400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:136995000-136996800	Enhancers	NHEK	skin
13	chr9:136995200-136996200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:136995200-136996200	Weak transcription	Esophagus	oesophagus
15	chr9:136995200-136996400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:136995400-136996600	Weak transcription	Right Atrium	heart
17	chr9:136995800-136996600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:136995800-136996600	Enhancers	Placenta	Placenta
19	chr9:136995800-136996800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:136995800-136996800	Flanking Active TSS	HepG2	liver
21	chr9:136996000-136996200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr9:136996000-136996200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:136996000-136996400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:136996000-136996400	Flanking Active TSS	Liver	Liver
25	chr9:136996000-136996400	Enhancers	Brain Cingulate Gyrus	brain
26	chr9:136996000-136996400	Enhancers	Colon Smooth Muscle	Colon
27	chr9:136996000-136996400	Enhancers	Fetal Stomach	stomach
28	chr9:136996000-136996400	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr9:136996000-136996400	Flanking Active TSS	A549	lung
30	chr9:136996000-136996400	Bivalent Enhancer	Osteobl	bone
31	chr9:136996000-136996600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:136996000-136996600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:136996000-136996600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:136996000-136996600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:136996000-136996600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr9:136996000-136996600	Enhancers	Colonic Mucosa	Colon
37	chr9:136996000-136996600	Enhancers	Fetal Intestine Small	intestine
38	chr9:136996000-136996600	Enhancers	Stomach Mucosa	stomach
39	chr9:136996000-136996800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:136996000-136996800	Enhancers	Fetal Heart	heart
41	chr9:136996000-136996800	Enhancers	Rectal Smooth Muscle	rectum
42	chr9:136996000-136996800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr9:136996000-136996800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr9:136996000-136996800	Flanking Active TSS	Hela-S3	cervix
45	chr9:136996000-136996800	Enhancers	HMEC	breast
46	chr9:136996000-136996800	Flanking Active TSS	HSMM	muscle
47	chr9:136996000-136996800	Flanking Active TSS	HSMMtube	muscle
48	chr9:136996000-136997000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr9:136996000-136997000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:136996000-136997000	Enhancers	Ovary	ovary

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