Variant report

Variant	rs73654534
Chromosome Location	chr9:97900970-97900971
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	CTCF	chr9:97900723-97901280	MCF-7	breast:	n/a	chr9:97901032-97901045
2	CTCF	chr9:97900940-97901090	MCF-7	breast:	n/a	chr9:97901032-97901045
3	CTCF	chr9:97900906-97901156	K562	blood:	n/a	chr9:97901032-97901045
4	CTCF	chr9:97900900-97901050	HEK293	kidney:	n/a	chr9:97901032-97901045
5	CTCF	chr9:97900897-97901137	NHEK	skin:	n/a	chr9:97901032-97901045
6	CTCF	chr9:97900937-97901087	MCF-7	breast:	n/a	chr9:97901032-97901045
7	SETDB1	chr9:97900951-97901577	U2OS	brain:	n/a	n/a
8	GATA3	chr9:97900559-97901265	SK-N-SH	brain:	n/a	chr9:97900851-97900872 chr9:97900854-97900870 chr9:97900858-97900865 chr9:97900858-97900867 chr9:97900855-97900865
9	GATA2	chr9:97900690-97901083	SH-SY5Y	brain:	n/a	chr9:97900851-97900872 chr9:97900854-97900870 chr9:97900858-97900865 chr9:97900858-97900867 chr9:97900855-97900865
10	EP300	chr9:97900818-97901046	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr9:97900900-97901050	A549	lung:	n/a	chr9:97901032-97901045
12	POLR2A	chr9:97900935-97901075	H1-hESC	embryonic stem cell:	n/a	n/a
13	EP300	chr9:97900546-97902616	SK-N-SH	brain:	n/a	chr9:97901443-97901457 chr9:97902179-97902193
14	CTCF	chr9:97900955-97901083	MCF-7	breast:	n/a	chr9:97901032-97901045
15	CTCF	chr9:97900937-97901101	MCF-7	breast:	n/a	chr9:97901032-97901045
16	CTCF	chr9:97900900-97901050	HEEpiC	esophagus:	n/a	chr9:97901032-97901045
17	CTCF	chr9:97900846-97901191	K562	blood:	n/a	chr9:97901032-97901045
18	CTCF	chr9:97900918-97901124	H1-hESC	embryonic stem cell:	n/a	chr9:97901032-97901045
19	CTCF	chr9:97900880-97901030	NHEK	skin:	n/a	n/a
20	MAX	chr9:97900742-97901258	MCF-7	breast:	n/a	n/a
21	CTCF	chr9:97900940-97901090	SK-N-SH_RA	brain:	n/a	chr9:97901032-97901045
22	EP300	chr9:97900705-97901060	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr9:97900920-97901070	BE2_C	brain:	n/a	chr9:97901032-97901045

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97895509..97898457-chr9:97900561..97904257,4	MCF-7	breast:
2	chr9:97900778..97902362-chr9:97906176..97907795,2	MCF-7	breast:

Variant related genes	Relation type
FANCC	TF binding region
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10453242	1.00[AFR][1000 genomes]
rs55651673	1.00[AFR][1000 genomes]
rs56025140	1.00[AFR][1000 genomes]
rs56134011	1.00[AFR][1000 genomes]
rs56280046	0.87[AFR][1000 genomes]
rs56354054	0.89[AFR][1000 genomes]
rs56737425	0.87[AFR][1000 genomes]
rs56761320	1.00[AFR][1000 genomes]
rs57312263	0.87[AFR][1000 genomes]
rs57883597	0.87[AFR][1000 genomes]
rs59611901	0.87[AFR][1000 genomes]
rs60346856	1.00[AFR][1000 genomes]
rs60497587	0.89[AFR][1000 genomes]
rs61462331	1.00[AFR][1000 genomes]
rs73654524	0.87[AFR][1000 genomes]
rs73654529	0.87[AFR][1000 genomes]
rs73654531	0.87[AFR][1000 genomes]
rs73654532	0.87[AFR][1000 genomes]
rs73654535	1.00[AFR][1000 genomes]
rs73654536	1.00[AFR][1000 genomes]
rs73654537	1.00[AFR][1000 genomes]
rs73654538	1.00[AFR][1000 genomes]
rs73654540	1.00[AFR][1000 genomes]
rs73654542	0.87[AFR][1000 genomes]
rs73654543	1.00[AFR][1000 genomes]
rs73654544	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97887400-97916400	Weak transcription	Thymus	Thymus
3	chr9:97890000-97906600	Weak transcription	Right Ventricle	heart
4	chr9:97890000-97919600	Weak transcription	Hela-S3	cervix
5	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:97890400-97902800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:97893200-97901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:97893800-97904800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:97893800-97905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:97893800-97905800	Weak transcription	Osteobl	bone
11	chr9:97893800-97906400	Weak transcription	Ovary	ovary
12	chr9:97893800-97912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:97893800-97918800	Weak transcription	Gastric	stomach
14	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
15	chr9:97894200-97906200	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:97894200-97909800	Weak transcription	A549	lung
17	chr9:97894200-97925600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:97894600-97905000	Weak transcription	Fetal Lung	lung
19	chr9:97894800-97905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:97895600-97901000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:97895800-97903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:97896000-97909800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:97896400-97910200	Weak transcription	Small Intestine	intestine
24	chr9:97896400-97918400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:97896400-97920000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:97896600-97905600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:97897000-97910000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:97897200-97901600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:97897200-97905000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr9:97897200-97905800	Weak transcription	HepG2	liver
31	chr9:97897200-97917400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:97897200-97919400	Weak transcription	GM12878-XiMat	blood
33	chr9:97897200-97920400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:97897600-97915400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:97899400-97901800	Strong transcription	Fetal Intestine Small	intestine
36	chr9:97899400-97903000	Enhancers	Liver	Liver
37	chr9:97899600-97901000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:97899600-97901200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr9:97900000-97901000	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr9:97900000-97901000	Enhancers	Psoas Muscle	Psoas
41	chr9:97900000-97901200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:97900000-97901800	Strong transcription	Primary T cells from cord blood	blood
43	chr9:97900000-97902000	Genic enhancers	Fetal Stomach	stomach
44	chr9:97900200-97901000	Enhancers	Fetal Muscle Leg	muscle
45	chr9:97900200-97901200	Enhancers	NHEK	skin
46	chr9:97900200-97901600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:97900400-97901200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:97900400-97901200	Enhancers	Brain Germinal Matrix	brain
49	chr9:97900400-97901600	Strong transcription	Fetal Intestine Large	intestine
50	chr9:97900400-97902000	Enhancers	Fetal Thymus	thymus

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