Variant report

Variant	rs9792913
Chromosome Location	chr1:153582403-153582404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153578781-153585928	U87	brain:	n/a	n/a
2	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:153578800-153582876	HUVEC	blood vessel:	n/a	n/a
4	EP300	chr1:153580431-153582499	MCF-7	breast:	n/a	chr1:153580785-153580799
5	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
6	CUX1	chr1:153581939-153582499	K562	blood:	n/a	n/a
7	POLR2A	chr1:153580843-153582539	U87	brain:	n/a	n/a
8	MAX	chr1:153580951-153582503	A549	lung:	n/a	n/a
9	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
10	TCF12	chr1:153581063-153583011	A549	lung:	n/a	chr1:153581524-153581534
11	POLR2A	chr1:153578024-153582691	HUVEC	blood vessel:	n/a	n/a
12	SMARCC2	chr1:153581117-153583552	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:153582348-153582517	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:153578145-153583129	HUVEC	blood vessel:	n/a	n/a
15	RCOR1	chr1:153580335-153582657	IMR90	lung:	n/a	n/a
16	BHLHE40	chr1:153581284-153582443	K562	blood:	n/a	chr1:153581428-153581444
17	POLR2A	chr1:153582332-153584090	HCT-116	colon:	n/a	n/a
18	GTF2F1	chr1:153582364-153583618	Hela-S3	cervix:	n/a	n/a
19	MAZ	chr1:153580631-153582545	IMR90	lung:	n/a	n/a
20	SMARCB1	chr1:153582344-153583905	Hela-S3	cervix:	n/a	n/a
21	SIN3AK20	chr1:153580199-153582486	MCF-7	breast:	n/a	n/a
22	POLR2A	chr1:153580980-153582424	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:153580356-153583237	HepG2	liver:	n/a	n/a
24	GATA2	chr1:153581193-153583269	HUVEC	blood vessel:	n/a	chr1:153581551-153581560 chr1:153582836-153582846
25	FOSL2	chr1:153581035-153582533	A549	lung:	n/a	n/a
26	MAZ	chr1:153581690-153582415	K562	blood:	n/a	n/a
27	POLR2A	chr1:153578333-153582858	HUVEC	blood vessel:	n/a	n/a
28	RCOR1	chr1:153582337-153582471	HepG2	liver:	n/a	n/a
29	SMARCC1	chr1:153580778-153586030	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:153577237-153583097	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr1:153579147-153585872	U87	brain:	n/a	n/a
32	GATA3	chr1:153580371-153582479	MCF-7	breast:	n/a	chr1:153581551-153581560 chr1:153580779-153580789
33	RCOR1	chr1:153581745-153582517	K562	blood:	n/a	n/a
34	POLR2A	chr1:153580843-153582511	U87	brain:	n/a	n/a
35	MAX	chr1:153580226-153582521	MCF-7	breast:	n/a	n/a
36	HEY1	chr1:153581096-153582595	HepG2	liver:	n/a	chr1:153581868-153581883
37	POLR2A	chr1:153580903-153583280	HCT-116	colon:	n/a	n/a
38	GATA3	chr1:153581905-153582513	T-47D	breast:	n/a	n/a
39	POLR2A	chr1:153580515-153583682	Hela-S3	cervix:	n/a	n/a
40	FOS	chr1:153581243-153583190	HUVEC	blood vessel:	n/a	chr1:153583120-153583129 chr1:153582957-153582965 chr1:153582957-153582964 chr1:153581551-153581562

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:
2	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
3	chr1:153581196..153582723-chr8:22366793..22368546,2	MCF-7	breast:
4	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
5	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
6	chr1:153581488..153584174-chr1:153940194..153943077,2	MCF-7	breast:
7	chr1:153580088..153583370-chr1:153747776..153750328,4	MCF-7	breast:
8	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
9	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
10	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
11	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
12	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
13	chr1:153325873..153327403-chr1:153582234..153585086,2	MCF-7	breast:
14	chr1:153581957..153582462-chr1:153739464..153739964,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000120910	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143570	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1046381	0.82[ASN][1000 genomes]
rs11497739	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11548102	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11548103	0.98[ASN][1000 genomes]
rs11548104	0.98[ASN][1000 genomes]
rs28416529	0.96[ASN][1000 genomes]
rs28518786	0.82[EUR][1000 genomes]
rs28754733	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35760493	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3806233	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4072425	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9330298	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9330299	0.98[ASN][1000 genomes]
rs9330300	0.96[ASN][1000 genomes]
rs9330301	0.96[ASN][1000 genomes]
rs9660679	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9699949	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9700179	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9700928	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9726753	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9729773	0.93[ASN][1000 genomes]
rs9792963	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9792967	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9793310	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs999418	0.96[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9792913	S100A14	cis	Esophagus Mucosa	GTEx
rs9792913	S100A13	cis	frontal cortex	BrainEAC
rs9792913	S100A13	cis	brain	BrainEAC
rs9792913	S100A13	cis	temporal cortex	BrainEAC
rs9792913	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs9792913	S100A13	cis	intralobular white matter	BrainEAC
rs9792913	CHTOP	cis	Muscle Skeletal	GTEx
rs9792913	RP1-178F15.4	cis	Thyroid	GTEx
rs9792913	S100A16	cis	Muscle Skeletal	GTEx
rs9792913	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs9792913	S100A13	cis	thalamus	BrainEAC
rs9792913	RP1-178F15.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153577800-153582800	Weak transcription	Small Intestine	intestine
2	chr1:153578800-153584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:153579400-153583600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:153579800-153583000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:153579800-153583600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:153580200-153584800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:153580400-153582800	Transcr. at gene 5' and 3'	NHLF	lung
8	chr1:153580400-153583200	Transcr. at gene 5' and 3'	NHEK	skin
9	chr1:153580600-153583200	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr1:153580600-153583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:153580800-153582600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:153580800-153582600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:153580800-153582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:153580800-153582800	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr1:153580800-153583000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:153580800-153583200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:153580800-153583200	Flanking Active TSS	Colonic Mucosa	Colon
18	chr1:153580800-153583600	Flanking Active TSS	Osteobl	bone
19	chr1:153581000-153583200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:153581000-153583400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:153581000-153584000	Enhancers	Colon Smooth Muscle	Colon
22	chr1:153581000-153584200	Enhancers	Fetal Lung	lung
23	chr1:153581200-153582600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr1:153581200-153584200	Enhancers	Gastric	stomach
25	chr1:153581200-153584200	Enhancers	Pancreas	Pancrea
26	chr1:153581400-153583600	Enhancers	Ovary	ovary
27	chr1:153581400-153584200	Enhancers	Left Ventricle	heart
28	chr1:153581400-153584800	Enhancers	Fetal Heart	heart
29	chr1:153581600-153582600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:153581600-153582800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:153581600-153583000	Transcr. at gene 5' and 3'	Esophagus	oesophagus
32	chr1:153581600-153583200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:153581600-153583200	Flanking Active TSS	HMEC	breast
34	chr1:153581600-153584000	Enhancers	Spleen	Spleen
35	chr1:153581800-153582600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:153581800-153582800	Genic enhancers	Fetal Stomach	stomach
37	chr1:153581800-153582800	Flanking Active TSS	HUVEC	blood vessel
38	chr1:153581800-153583200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr1:153581800-153583600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:153581800-153583600	Enhancers	Placenta	Placenta
41	chr1:153581800-153583600	Flanking Active TSS	A549	lung
42	chr1:153581800-153584200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:153581800-153584200	Enhancers	Fetal Muscle Trunk	muscle
44	chr1:153581800-153584200	Enhancers	Fetal Muscle Leg	muscle
45	chr1:153581800-153584200	Enhancers	Right Atrium	heart
46	chr1:153581800-153584200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr1:153581800-153584400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:153582000-153582600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:153582000-153582800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr1:153582000-153582800	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links