Variant report

Variant	rs9699949
Chromosome Location	chr1:153583986-153583987
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	POLR2A	chr1:153578781-153585928	U87	brain:	n/a	n/a
2	POLR2A	chr1:153583700-153584543	U87	brain:	n/a	n/a
3	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
4	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
5	STAT3	chr1:153583950-153584152	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:153583694-153584347	HCT-116	colon:	n/a	n/a
9	MAX	chr1:153582672-153584061	Hela-S3	cervix:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
10	MAFK	chr1:153583855-153584174	IMR90	lung:	n/a	n/a
11	MAFK	chr1:153583959-153584083	HepG2	liver:	n/a	n/a
12	TBP	chr1:153583391-153583992	Hela-S3	cervix:	n/a	n/a
13	ZKSCAN1	chr1:153583471-153584538	Hela-S3	cervix:	n/a	n/a
14	FOS	chr1:153583423-153584211	MCF10A-Er-Src	breast:	n/a	n/a
15	MAFK	chr1:153583889-153584861	Hela-S3	cervix:	n/a	n/a
16	MAFF	chr1:153583959-153584017	K562	blood:	n/a	n/a
17	POLR2A	chr1:153582332-153584090	HCT-116	colon:	n/a	n/a
18	FOS	chr1:153583377-153584159	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:153583704-153585183	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr1:153583367-153584315	Hela-S3	cervix:	n/a	chr1:153583505-153583514 chr1:153583503-153583512
21	POLR2A	chr1:153583700-153584414	U87	brain:	n/a	n/a
22	MYC	chr1:153582822-153584034	MCF10A-Er-Src	breast:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
23	MAX	chr1:153582564-153584929	A549	lung:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153584570-153584580 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
24	SMARCC1	chr1:153580778-153586030	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:153579147-153585872	U87	brain:	n/a	n/a
26	FOS	chr1:153583390-153584194	MCF10A-Er-Src	breast:	n/a	n/a
27	MAZ	chr1:153582872-153584213	Hela-S3	cervix:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
28	FOS	chr1:153583389-153584213	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:153582663-153584342	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr1:153583390-153584615	HepG2	liver:	n/a	n/a
31	MYC	chr1:153582849-153584164	MCF10A-Er-Src	breast:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514

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	chr1:153582758..153584340-chr1:153640785..153643279,2	K562	blood:
5	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
6	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
7	chr1:153329994..153332051-chr1:153582439..153585039,2	MCF-7	breast:
8	chr1:153581488..153584174-chr1:153940194..153943077,2	MCF-7	breast:
9	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
10	chr1:153524896..153526956-chr1:153582984..153585542,2	MCF-7	breast:
11	chr1:153325873..153327403-chr1:153582234..153585086,2	MCF-7	breast:
12	chr1:153488074..153490383-chr1:153582465..153584577,2	MCF-7	breast:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1046381	0.82[ASN][1000 genomes]
rs11497739	0.95[ASN][1000 genomes]
rs11548102	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548103	0.95[ASN][1000 genomes]
rs11548104	0.95[ASN][1000 genomes]
rs28416529	0.94[ASN][1000 genomes]
rs28754733	0.96[ASN][1000 genomes]
rs35760493	0.95[ASN][1000 genomes]
rs35890901	0.83[ASN][1000 genomes]
rs3806233	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4072425	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330298	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330299	0.95[ASN][1000 genomes]
rs9330300	0.94[ASN][1000 genomes]
rs9330301	0.94[ASN][1000 genomes]
rs9660679	0.95[ASN][1000 genomes]
rs9700179	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9700928	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9726753	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9729773	0.94[ASN][1000 genomes]
rs9792913	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792963	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792967	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9793310	0.95[ASN][1000 genomes]
rs999418	0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9699949	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs9699949	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs9699949	S100A14	cis	Esophagus Mucosa	GTEx
rs9699949	S100A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153578800-153584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153580200-153584800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:153581000-153584000	Enhancers	Colon Smooth Muscle	Colon
4	chr1:153581000-153584200	Enhancers	Fetal Lung	lung
5	chr1:153581200-153584200	Enhancers	Gastric	stomach
6	chr1:153581200-153584200	Enhancers	Pancreas	Pancrea
7	chr1:153581400-153584200	Enhancers	Left Ventricle	heart
8	chr1:153581400-153584800	Enhancers	Fetal Heart	heart
9	chr1:153581600-153584000	Enhancers	Spleen	Spleen
10	chr1:153581800-153584200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:153581800-153584200	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:153581800-153584200	Enhancers	Fetal Muscle Leg	muscle
13	chr1:153581800-153584200	Enhancers	Right Atrium	heart
14	chr1:153581800-153584200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr1:153581800-153584400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:153582000-153584000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:153582000-153584000	Enhancers	Brain Anterior Caudate	brain
18	chr1:153582000-153584000	Enhancers	Fetal Intestine Large	intestine
19	chr1:153582000-153584200	Weak transcription	Aorta	Aorta
20	chr1:153582000-153584200	Enhancers	Lung	lung
21	chr1:153582000-153584400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:153582200-153584000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:153582200-153584200	Enhancers	Liver	Liver
24	chr1:153582200-153584600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:153582200-153584600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:153582200-153585000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:153582200-153585200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:153582400-153584000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:153582400-153584000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:153582400-153584000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:153582400-153584000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:153582400-153584000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:153582400-153584000	Weak transcription	Brain Angular Gyrus	brain
34	chr1:153582400-153584000	Enhancers	K562	blood
35	chr1:153582400-153584200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:153582400-153584200	Enhancers	Right Ventricle	heart
37	chr1:153582400-153584600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:153582400-153584600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:153582600-153584200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:153582600-153584400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:153582600-153584600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:153582800-153584000	Enhancers	Small Intestine	intestine
43	chr1:153582800-153584200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:153582800-153584200	Enhancers	Fetal Stomach	stomach
45	chr1:153582800-153585600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:153582800-153591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:153583000-153584000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:153583000-153584000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:153583000-153584400	Flanking Active TSS	Hela-S3	cervix
50	chr1:153583000-153589000	Active TSS	Esophagus	oesophagus

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