Variant report

Variant	rs58433601
Chromosome Location	chr9:96713374-96713375
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:96713310-96713838	MCF-7	breast:	n/a	n/a
2	SUZ12	chr9:96709708-96717433	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr9:96712976-96714057	NB4	blood:	n/a	n/a
4	GABPA	chr9:96713258-96713902	MCF-7	breast:	n/a	chr9:96713831-96713838
5	ELF1	chr9:96713369-96713708	GM12878	blood:	n/a	n/a
6	CTBP2	chr9:96710652-96717425	H1-hESC	embryonic stem cell:	n/a	n/a
7	NR2F2	chr9:96713340-96713923	MCF-7	breast:	n/a	n/a
8	ELF1	chr9:96713025-96713967	MCF-7	breast:	n/a	chr9:96713327-96713336
9	POLR2A	chr9:96713166-96714239	NB4	blood:	n/a	n/a
10	MAX	chr9:96712975-96713977	MCF-7	breast:	n/a	n/a
11	E2F6	chr9:96713286-96713882	H1-hESC	embryonic stem cell:	n/a	chr9:96713322-96713332
12	GABPA	chr9:96713130-96713922	MCF-7	breast:	n/a	chr9:96713831-96713838
13	MAX	chr9:96713024-96713974	NB4	blood:	n/a	n/a
14	GABPA	chr9:96713323-96713754	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr9:96713127-96713862	MCF-7	breast:	n/a	n/a
16	POLR2A	chr9:96711482-96713707	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96710015..96712729-chr9:96712737..96714256,2	MCF-7	breast:
2	chr9:96711387..96714258-chr9:96716250..96718266,3	K562	blood:
3	chr9:96706258..96707958-chr9:96711820..96714339,2	MCF-7	breast:
4	chr9:96443001..96444886-chr9:96710905..96713769,2	MCF-7	breast:
5	chr9:96701424..96703213-chr9:96710660..96713568,2	MCF-7	breast:
6	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:
7	chr9:96664499..96666537-chr9:96711318..96713769,2	MCF-7	breast:
8	chr9:96338597..96340419-chr9:96710594..96713429,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235601	TF binding region
ENSG00000197724	Chromatin interaction
ENSG00000131668	Chromatin interaction
ENSG00000235601	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs56793884	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57483569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60329608	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73518275	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96710600-96713800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:96711600-96715600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
3	chr9:96712600-96714000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:96712800-96713400	Bivalent Enhancer	Fetal Lung	lung
5	chr9:96712800-96713400	Enhancers	Spleen	Spleen
6	chr9:96712800-96713600	Flanking Active TSS	Hela-S3	cervix
7	chr9:96712800-96713800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
8	chr9:96712800-96714800	Bivalent/Poised TSS	HSMM	muscle
9	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
11	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
12	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
13	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
14	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
17	chr9:96713000-96713400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
18	chr9:96713000-96713400	Flanking Active TSS	Right Ventricle	heart
19	chr9:96713000-96713600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:96713000-96713600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
21	chr9:96713000-96713600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
22	chr9:96713000-96713600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
23	chr9:96713000-96713600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:96713000-96713600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:96713000-96713600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
26	chr9:96713000-96713600	Bivalent Enhancer	Fetal Thymus	thymus
27	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
28	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
29	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
33	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
34	chr9:96713000-96713800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
35	chr9:96713000-96714200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
36	chr9:96713000-96714400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
37	chr9:96713000-96714400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr9:96713000-96714600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
39	chr9:96713000-96714800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr9:96713000-96715800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
41	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
42	chr9:96713200-96713400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
43	chr9:96713200-96713400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:96713200-96713400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:96713200-96713400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:96713200-96713400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:96713200-96713400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
48	chr9:96713200-96713400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
49	chr9:96713200-96713400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
50	chr9:96713200-96713400	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon

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