Variant report

Variant	rs61358915
Chromosome Location	chr9:97901513-97901514
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	SETDB1	chr9:97900951-97901577	U2OS	brain:	n/a	n/a
2	EP300	chr9:97900546-97902616	SK-N-SH	brain:	n/a	chr9:97901443-97901457 chr9:97902179-97902193

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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf3-3	chr9:97901185-97902154	ucscGeneNc_uc004avy_2

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2404458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3780566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647430	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647464	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647474	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647487	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647510	1.00[AFR][1000 genomes]
rs4647516	1.00[AFR][1000 genomes]
rs57641389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60228132	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73528484	1.00[AFR][1000 genomes]
rs73528487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534874	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534875	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534896	0.82[AFR][1000 genomes]
rs73539228	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73539285	1.00[AMR][1000 genomes]
rs7859625	1.00[AFR][1000 genomes];1.00[AMR][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:61 , 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	chr9:97895800-97903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:97896000-97909800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:97896400-97910200	Weak transcription	Small Intestine	intestine
23	chr9:97896400-97918400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:97896400-97920000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:97896600-97905600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:97897000-97910000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:97897200-97901600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:97897200-97905000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr9:97897200-97905800	Weak transcription	HepG2	liver
30	chr9:97897200-97917400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:97897200-97919400	Weak transcription	GM12878-XiMat	blood
32	chr9:97897200-97920400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr9:97897600-97915400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:97899400-97901800	Strong transcription	Fetal Intestine Small	intestine
35	chr9:97899400-97903000	Enhancers	Liver	Liver
36	chr9:97900000-97901800	Strong transcription	Primary T cells from cord blood	blood
37	chr9:97900000-97902000	Genic enhancers	Fetal Stomach	stomach
38	chr9:97900200-97901600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:97900400-97901600	Strong transcription	Fetal Intestine Large	intestine
40	chr9:97900400-97902000	Enhancers	Fetal Thymus	thymus
41	chr9:97900400-97902400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:97900600-97919600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr9:97900800-97901800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:97900800-97901800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:97900800-97903400	Weak transcription	Spleen	Spleen
46	chr9:97900800-97905600	Weak transcription	Esophagus	oesophagus
47	chr9:97900800-97910600	Weak transcription	Lung	lung
48	chr9:97900800-97930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:97901000-97901600	Enhancers	H1 Cell Line	embryonic stem cell
50	chr9:97901000-97901600	Weak transcription	Fetal Muscle Trunk	muscle

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