Variant report

Variant	rs408200
Chromosome Location	chr9:972476-972477
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	MAX	chr9:971355-972596	H1-hESC	embryonic stem cell:	n/a	chr9:972357-972367
2	EGR1	chr9:971959-972720	H1-hESC	embryonic stem cell:	n/a	chr9:972403-972412 chr9:972044-972054 chr9:972045-972055
3	SUZ12	chr9:972207-974176	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTBP2	chr9:971617-973784	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:971960-972483	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr9:972353-972694	H1-hESC	embryonic stem cell:	n/a	n/a
7	BACH1	chr9:972119-972583	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr9:971431-973249	H1-hESC	embryonic stem cell:	n/a	chr9:973088-973095 chr9:973087-973096 chr9:972357-972367
9	SIN3A	chr9:971990-973192	H1-hESC	embryonic stem cell:	n/a	chr9:972941-972952
10	RAD21	chr9:972172-972507	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr9:970320-973357	H1-hESC	embryonic stem cell:	n/a	chr9:972045-972054 chr9:972887-972895 chr9:972135-972146 chr9:972169-972178 chr9:972887-972895 chr9:971791-971798 chr9:973012-973024
12	SP1	chr9:971924-972741	H1-hESC	embryonic stem cell:	n/a	chr9:972075-972084 chr9:972046-972055 chr9:972045-972054 chr9:972046-972055 chr9:972044-972056 chr9:972352-972366 chr9:972045-972055 chr9:972044-972056 chr9:972076-972085 chr9:972041-972055 chr9:972386-972393 chr9:972045-972055
13	SUZ12	chr9:972157-978361	NT2-D1	testis:	n/a	n/a
14	ZNF143	chr9:971964-972949	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:971648..973169-chr9:976261..977886,2	MCF-7	breast:
2	chr9:970488..973347-chr9:974585..976403,2	K562	blood:
3	chr9:962191..965396-chr9:970150..972525,3	MCF-7	breast:
4	chr9:959751..962676-chr9:970259..973174,2	K562	blood:

Variant related genes	Relation type
DMRT3	TF binding region
ENSG00000064218	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs279879	0.82[JPT][hapmap]
rs399000	0.88[ASN][1000 genomes]
rs454101	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv892000	chr9:678951-972476	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:969400-973200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr9:969400-973400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:969600-973200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr9:969600-973400	Bivalent Enhancer	Lung	lung
5	chr9:969800-973200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:969800-973200	Bivalent Enhancer	Fetal Lung	lung
7	chr9:970600-973000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:970600-973000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:970800-972800	Bivalent/Poised TSS	Psoas Muscle	Psoas
10	chr9:971200-973400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:971400-972600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr9:971400-972800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr9:971400-972800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr9:971400-972800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr9:971400-973000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:971400-973000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr9:971400-973200	Bivalent Enhancer	Fetal Heart	heart
18	chr9:971400-973600	Bivalent Enhancer	Liver	Liver
19	chr9:971400-973800	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr9:971600-972600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
21	chr9:971600-972600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:971600-972600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:971600-972600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:971600-972600	Active TSS	Aorta	Aorta
25	chr9:971600-972800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:971600-972800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:971600-972800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
28	chr9:971600-972800	Flanking Bivalent TSS/Enh	Thymus	Thymus
29	chr9:971600-973000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:971600-973200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:971600-973400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
32	chr9:971600-973800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
33	chr9:971800-972600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:971800-972600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:971800-972600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:971800-972600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
37	chr9:971800-972800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr9:971800-972800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:971800-972800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr9:971800-973800	Active TSS	Right Atrium	heart
41	chr9:972000-972600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr9:972000-972600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
43	chr9:972000-972600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
44	chr9:972000-972600	Bivalent/Poised TSS	NHEK	skin
45	chr9:972000-973000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
46	chr9:972000-973000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr9:972000-973000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr9:972200-972600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:972200-972600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
50	chr9:972200-972600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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