Variant report

Variant	rs279911
Chromosome Location	chr9:973695-973696
allele	G/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	chr9:973349-975160	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr9:972207-974176	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr9:971617-973784	H1-hESC	embryonic stem cell:	n/a	n/a
4	SETDB1	chr9:973442-973984	U2OS	brain:	n/a	n/a
5	ZNF263	chr9:973488-973970	HEK293-T-REx	kidney:	n/a	n/a
6	POLR2A	chr9:973454-973857	H1-neurons	neurons:	n/a	n/a
7	SUZ12	chr9:972157-978361	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:967263..969449-chr9:973261..974895,2	MCF-7	breast:
2	chr9:968342..970313-chr9:973554..975096,2	K562	blood:

Variant related genes	Relation type
DMRT3	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10816147	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816154	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10816155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166789	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs279882	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs279884	0.88[EUR][1000 genomes]
rs279886	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs279890	0.90[EUR][1000 genomes]
rs279891	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs279910	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34893137	0.85[EUR][1000 genomes]
rs417260	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs438293	0.85[EUR][1000 genomes]
rs438294	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs541568	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs604973	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv429977	chr9:584087-983301	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv831491	chr9:794113-974142	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1034070	chr9:911265-1152351	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv2755928	chr9:924525-985979	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv892013	chr9:943611-1047343	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1018926	chr9:965006-1014141	Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv892014	chr9:972476-1032153	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:971400-973800	Bivalent Enhancer	Stomach Mucosa	stomach
2	chr9:971600-973800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr9:971800-973800	Active TSS	Right Atrium	heart
4	chr9:972200-973800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr9:972400-973800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:972400-973800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr9:972600-974000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr9:973000-973800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
9	chr9:973000-976200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:973200-973800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr9:973200-974400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
12	chr9:973200-976000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr9:973400-973800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:973400-973800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr9:973400-973800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
16	chr9:973400-974000	Bivalent/Poised TSS	NHEK	skin
17	chr9:973400-975400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr9:973600-973800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr9:973600-973800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:973600-974000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:973600-974400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:973600-974600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
23	chr9:973600-975000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr9:973600-975200	Weak transcription	Pancreas	Pancrea

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