Variant report

Variant	rs9562794
Chromosome Location	chr13:48576706-48576707
allele	C/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	RCOR1	chr13:48574590-48576716	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136159	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10397	0.87[EUR][1000 genomes]
rs11617714	0.90[ASN][1000 genomes]
rs11617894	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11618304	0.90[ASN][1000 genomes]
rs12561235	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13243	0.87[EUR][1000 genomes]
rs17071169	0.90[ASN][1000 genomes]
rs2025703	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41284209	0.90[ASN][1000 genomes]
rs4477588	0.83[EUR][1000 genomes]
rs45465203	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56097393	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385117	0.87[EUR][1000 genomes]
rs7324919	0.87[EUR][1000 genomes]
rs7326861	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335662	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337521	0.90[ASN][1000 genomes]
rs7981492	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562784	0.87[EUR][1000 genomes]
rs9562785	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562786	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562790	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9562791	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562795	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562797	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562798	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567956	0.86[EUR][1000 genomes]
rs9567957	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567966	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567967	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567971	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567974	0.90[ASN][1000 genomes]
rs9567975	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567977	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567978	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567981	0.90[ASN][1000 genomes]
rs9567982	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567983	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567985	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567990	0.90[ASN][1000 genomes]
rs9634678	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48576000-48576800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr13:48576000-48576800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:48576000-48576800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:48576000-48576800	Enhancers	Fetal Brain Male	brain
5	chr13:48576000-48576800	Enhancers	HMEC	breast
6	chr13:48576000-48577800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr13:48576000-48578000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr13:48576000-48578200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:48576000-48578400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:48576000-48580200	Weak transcription	HSMM	muscle
11	chr13:48576000-48582800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr13:48576000-48583200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:48576000-48583600	Weak transcription	HSMMtube	muscle
16	chr13:48576000-48583800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:48576000-48587000	Weak transcription	Primary B cells from cord blood	blood
18	chr13:48576000-48587000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr13:48576000-48588400	Weak transcription	Fetal Intestine Large	intestine
20	chr13:48576000-48589800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:48576000-48590800	Weak transcription	Gastric	stomach
22	chr13:48576000-48603600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr13:48576000-48604000	Weak transcription	Primary T cells from cord blood	blood
24	chr13:48576000-48604800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr13:48576000-48604800	Weak transcription	Fetal Stomach	stomach
26	chr13:48576000-48604800	Weak transcription	Thymus	Thymus
27	chr13:48576000-48610800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr13:48576000-48611400	Weak transcription	Left Ventricle	heart
29	chr13:48576200-48576800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:48576200-48576800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:48576200-48578400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:48576200-48592000	Weak transcription	Fetal Intestine Small	intestine
33	chr13:48576400-48576800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr13:48576400-48576800	Flanking Active TSS	Hela-S3	cervix
35	chr13:48576400-48576800	Enhancers	HepG2	liver
36	chr13:48576400-48577400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr13:48576400-48577800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:48576400-48578200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr13:48576400-48589000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr13:48576400-48605000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr13:48576600-48576800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr13:48576600-48576800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr13:48576600-48576800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:48576600-48577000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:48576600-48577000	Enhancers	A549	lung
46	chr13:48576600-48577400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr13:48576600-48577400	Enhancers	NHEK	skin
48	chr13:48576600-48577600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr13:48576600-48583200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr13:48576600-48583600	Weak transcription	Placenta	Placenta

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