Variant report

Variant	rs11486185
Chromosome Location	chr1:153584242-153584243
allele	G/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	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	POLR2A	chr1:153583694-153584347	HCT-116	colon:	n/a	n/a
6	ZKSCAN1	chr1:153583471-153584538	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr1:153583889-153584861	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:153584098-153585176	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:153583704-153585183	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr1:153583367-153584315	Hela-S3	cervix:	n/a	chr1:153583505-153583514 chr1:153583503-153583512
11	POLR2A	chr1:153583700-153584414	U87	brain:	n/a	n/a
12	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
13	SMARCC1	chr1:153580778-153586030	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:153579147-153585872	U87	brain:	n/a	n/a
15	POLR2A	chr1:153582663-153584342	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:153583390-153584615	HepG2	liver:	n/a	n/a

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	chr1:153584203..153584864-chr16:30076780..30077582,2	Hela-S3	cervix:
8	chr1:153329994..153332051-chr1:153582439..153585039,2	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	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
13	chr1:153488074..153490383-chr1:153582465..153584577,2	MCF-7	breast:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000273026	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000238279	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs28444667	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57058331	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59005288	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61083533	0.93[AFR][1000 genomes]
rs61296485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74115501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118304	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118305	0.93[AFR][1000 genomes]
rs74118306	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118307	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118314	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118316	1.00[AMR][1000 genomes]
rs74118317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118318	1.00[AMR][1000 genomes]
rs7543851	1.00[CHB][hapmap]
rs9700870	0.81[AFR][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

No data

Chromatin state (count:98 , 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	chr1:153581400-153584800	Enhancers	Fetal Heart	heart
4	chr1:153581800-153584400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:153582000-153584400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:153582200-153584600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:153582200-153584600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:153582200-153585000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:153582200-153585200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:153582400-153584600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:153582400-153584600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:153582600-153584400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:153582600-153584600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:153582800-153585600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:153582800-153591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:153583000-153584400	Flanking Active TSS	Hela-S3	cervix
17	chr1:153583000-153589000	Active TSS	Esophagus	oesophagus
18	chr1:153583200-153585600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr1:153583200-153585600	Active TSS	HSMM	muscle
20	chr1:153583200-153585800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:153583200-153585800	Active TSS	HMEC	breast
22	chr1:153583200-153585800	Active TSS	NHLF	lung
23	chr1:153583200-153586000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:153583600-153584400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:153583600-153584600	Weak transcription	Placenta	Placenta
26	chr1:153583600-153584800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:153583600-153585600	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr1:153583600-153585800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:153583600-153585800	Active TSS	A549	lung
30	chr1:153583600-153590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:153583800-153584400	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr1:153583800-153584400	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr1:153583800-153584400	Flanking Active TSS	Stomach Mucosa	stomach
34	chr1:153583800-153584400	Flanking Active TSS	Osteobl	bone
35	chr1:153583800-153584600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr1:153583800-153584600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr1:153583800-153584800	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr1:153583800-153585200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr1:153583800-153585200	Transcr. at gene 5' and 3'	NHEK	skin
40	chr1:153583800-153585400	Active TSS	Brain Substantia Nigra	brain
41	chr1:153583800-153585600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:153583800-153585600	Active TSS	Brain Hippocampus Middle	brain
43	chr1:153583800-153586200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:153584000-153584400	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr1:153584000-153584400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:153584000-153584600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:153584000-153584600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:153584000-153584600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:153584000-153584600	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr1:153584000-153584600	Weak transcription	Spleen	Spleen

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