Variant report

Variant	rs9700928
Chromosome Location	chr1:153584986-153584987
allele	A/C
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	POLR2A	chr1:153578781-153585928	U87	brain:	n/a	n/a
2	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr1:153583230-153586398	IMR90	lung:	n/a	chr1:153583503-153583514 chr1:153584946-153584956 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153585185-153585195 chr1:153583502-153583515 chr1:153584570-153584580 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514 chr1:153586089-153586098
4	POLR2A	chr1:153584432-153586236	MCF-7	breast:	n/a	n/a
5	SP1	chr1:153584935-153585868	A549	lung:	n/a	chr1:153585229-153585243 chr1:153585669-153585683 chr1:153584946-153584958 chr1:153584946-153584958 chr1:153584948-153584957 chr1:153585229-153585238
6	ELK1	chr1:153584900-153585043	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr1:153584896-153585068	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:153584925-153585719	HepG2	liver:	n/a	n/a
9	STAT3	chr1:153584673-153584990	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr1:153584658-153585059	Hela-S3	cervix:	n/a	n/a
11	ZBTB7A	chr1:153584706-153585836	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr1:153584716-153585023	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:153584098-153585176	Hela-S3	cervix:	n/a	n/a
14	MAZ	chr1:153584585-153586025	Hela-S3	cervix:	n/a	chr1:153584946-153584956 chr1:153585185-153585195
15	HEY1	chr1:153584918-153585619	HepG2	liver:	n/a	n/a
16	GTF2F1	chr1:153584898-153584988	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:153584791-153585168	HCT-116	colon:	n/a	n/a
18	SMC3	chr1:153584650-153585977	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:153583704-153585183	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:153584631-153585698	HepG2	liver:	n/a	n/a
21	SMARCC1	chr1:153580778-153586030	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:153579147-153585872	U87	brain:	n/a	n/a
23	POLR2A	chr1:153584738-153587038	HCT-116	colon:	n/a	n/a
24	SMARCB1	chr1:153584281-153586054	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr1:153584793-153585882	A549	lung:	n/a	chr1:153585856-153585864

No.	Distal block	Cell Line	Cell type
1	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
2	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:
3	chr1:153361209..153363367-chr1:153582574..153585428,2	MCF-7	breast:
4	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
5	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
6	chr1:153329994..153332051-chr1:153582439..153585039,2	MCF-7	breast:
7	chr1:153584270..153586809-chr1:153629991..153631660,2	MCF-7	breast:
8	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
9	chr1:153524896..153526956-chr1:153582984..153585542,2	MCF-7	breast:
10	chr1:153325873..153327403-chr1:153582234..153585086,2	MCF-7	breast:
11	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143578	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1046381	0.82[ASN][1000 genomes]
rs10797096	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10908848	0.82[CEU][hapmap]
rs11265625	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11497739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11548102	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11548103	0.98[ASN][1000 genomes]
rs11548104	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11588347	0.81[EUR][1000 genomes]
rs12139953	0.80[EUR][1000 genomes]
rs12730186	0.83[EUR][1000 genomes]
rs28416529	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28518786	0.86[EUR][1000 genomes]
rs28754733	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35760493	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806233	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3862047	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4072425	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4515830	0.83[CEU][hapmap]
rs4845563	0.81[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs4845564	0.81[EUR][1000 genomes]
rs55772653	0.82[EUR][1000 genomes]
rs66721814	0.83[EUR][1000 genomes]
rs6674929	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs9330298	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9330299	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9330300	0.96[ASN][1000 genomes]
rs9330301	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9660679	0.99[ASN][1000 genomes]
rs9662664	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs9699949	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9700179	0.84[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9726753	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9729773	0.93[ASN][1000 genomes]
rs9792913	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792963	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9792967	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9793310	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9700928	RP1-178F15.4	cis	Thyroid	GTEx
rs9700928	S100A13	cis	lymphoblastoid	seeQTL
rs9700928	S100A2	cis	cerebellum	SCAN
rs9700928	S100A16	cis	parietal	SCAN
rs9700928	S100A13	cis	parietal	SCAN
rs9700928	S100A16	cis	cerebellum	SCAN
rs9700928	ZNF687	cis	cerebellum	SCAN
rs9700928	S100A9	cis	parietal	SCAN
rs9700928	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs9700928	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs9700928	S100A14	cis	Esophagus Mucosa	GTEx
rs9700928	S100A16	cis	Muscle Skeletal	GTEx
rs9700928	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs9700928	CTSS	cis	parietal	SCAN
rs9700928	S100A10	cis	cerebellum	SCAN
rs9700928	CHTOP	cis	Muscle Skeletal	GTEx
rs9700928	SLC27A3	cis	cerebellum	SCAN
rs9700928	PGLYRP4	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153582200-153585000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:153582200-153585200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:153582800-153585600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:153582800-153591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:153583000-153589000	Active TSS	Esophagus	oesophagus
6	chr1:153583200-153585600	Active TSS	Muscle Satellite Cultured Cells	--
7	chr1:153583200-153585600	Active TSS	HSMM	muscle
8	chr1:153583200-153585800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:153583200-153585800	Active TSS	HMEC	breast
10	chr1:153583200-153585800	Active TSS	NHLF	lung
11	chr1:153583200-153586000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:153583600-153585600	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr1:153583600-153585800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:153583600-153585800	Active TSS	A549	lung
15	chr1:153583600-153590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:153583800-153585200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:153583800-153585200	Transcr. at gene 5' and 3'	NHEK	skin
18	chr1:153583800-153585400	Active TSS	Brain Substantia Nigra	brain
19	chr1:153583800-153585600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:153583800-153585600	Active TSS	Brain Hippocampus Middle	brain
21	chr1:153583800-153586200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:153584000-153585000	Active TSS	Brain Angular Gyrus	brain
23	chr1:153584000-153585000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
24	chr1:153584000-153585000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:153584000-153585000	Flanking Active TSS	HepG2	liver
26	chr1:153584000-153585200	Active TSS	Colonic Mucosa	Colon
27	chr1:153584000-153585600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:153584000-153585600	Active TSS	Brain Anterior Caudate	brain
29	chr1:153584000-153585600	Active TSS	Brain Cingulate Gyrus	brain
30	chr1:153584000-153585800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:153584000-153585800	Active TSS	Ovary	ovary
32	chr1:153584000-153585800	Active TSS	NHDF-Ad	bronchial
33	chr1:153584000-153588600	Weak transcription	K562	blood
34	chr1:153584200-153585000	Flanking Active TSS	Liver	Liver
35	chr1:153584200-153585000	Flanking Active TSS	Right Ventricle	heart
36	chr1:153584200-153585400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:153584200-153585600	Active TSS	Aorta	Aorta
38	chr1:153584200-153585600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:153584200-153585600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr1:153584200-153585600	Active TSS	Gastric	stomach
41	chr1:153584200-153585600	Active TSS	Lung	lung
42	chr1:153584200-153585600	Active TSS	Small Intestine	intestine
43	chr1:153584200-153585600	Active TSS	HSMMtube	muscle
44	chr1:153584200-153585600	Active TSS	HUVEC	blood vessel
45	chr1:153584200-153585800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:153584200-153585800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr1:153584200-153585800	Enhancers	Fetal Brain Male	brain
48	chr1:153584200-153585800	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr1:153584200-153585800	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr1:153584200-153585800	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links