Variant report

Variant	rs689462
Chromosome Location	chr1:186651083-186651084
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	RFX5	chr1:186651005-186652278	Hela-S3	cervix:	n/a	n/a
2	FOS	chr1:186650959-186651273	MCF10A-Er-Src	breast:	n/a	chr1:186651220-186651229
3	POLR2A	chr1:186650697-186651259	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr1:186650990-186651351	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr1:186650981-186651317	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:186648078-186651650	IMR90	lung:	n/a	n/a
7	STAT3	chr1:186650989-186651207	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:186646993-186651195	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr1:186648686-186651449	A549	lung:	n/a	chr1:186651134-186651142
10	BRCA1	chr1:186650113-186652019	Hela-S3	cervix:	n/a	chr1:186650261-186650268 chr1:186651446-186651453
11	FOS	chr1:186650954-186651268	MCF10A-Er-Src	breast:	n/a	chr1:186651220-186651229
12	FOS	chr1:186651010-186651232	MCF10A-Er-Src	breast:	n/a	chr1:186651220-186651229
13	SMC3	chr1:186651020-186651233	Hela-S3	cervix:	n/a	n/a
14	MYC	chr1:186650959-186651312	MCF10A-Er-Src	breast:	n/a	n/a
15	TBP	chr1:186648845-186652253	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr1:186651007-186651189	MCF10A-Er-Src	breast:	n/a	n/a
17	CEBPB	chr1:186650968-186651298	IMR90	lung:	n/a	chr1:186651144-186651155 chr1:186651144-186651157
18	CEBPB	chr1:186650957-186651350	Hela-S3	cervix:	n/a	chr1:186651144-186651155 chr1:186651144-186651157
19	MAFK	chr1:186650924-186651429	Hela-S3	cervix:	n/a	n/a
20	E2F4	chr1:186650903-186651169	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:186651000-186651196	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:186650961-186651287	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:186647207-186651362	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr1:186650995-186651335	A549	lung:	n/a	chr1:186651144-186651155 chr1:186651144-186651157
25	STAT3	chr1:186650943-186651284	MCF10A-Er-Src	breast:	n/a	chr1:186650977-186651000
26	EP300	chr1:186650945-186651508	Hela-S3	cervix:	n/a	chr1:186651145-186651159

Variant related genes	Relation type
PTGS2	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10798055	1.00[ASN][1000 genomes]
rs11567835	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11567836	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116711	1.00[ASN][1000 genomes]
rs12117451	1.00[ASN][1000 genomes]
rs12119919	1.00[ASN][1000 genomes]
rs12144220	1.00[ASN][1000 genomes]
rs12720491	1.00[ASN][1000 genomes]
rs13376484	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16825688	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4648282	0.93[EUR][1000 genomes]
rs4648284	0.93[EUR][1000 genomes]
rs4648298	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4648311	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650701	1.00[ASN][1000 genomes]
rs59638687	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59873426	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61516014	1.00[EUR][1000 genomes]
rs689468	0.93[EUR][1000 genomes]
rs689469	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689470	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs74134717	1.00[EUR][1000 genomes]
rs7520374	0.88[EUR][1000 genomes]
rs7523981	1.00[ASN][1000 genomes]
rs766400	1.00[ASN][1000 genomes]
rs964570	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186647000-186652000	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:186647800-186651800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:186648000-186651200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:186648000-186651600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:186648000-186651800	Active TSS	Colon Smooth Muscle	Colon
6	chr1:186648000-186651800	Active TSS	NHDF-Ad	bronchial
7	chr1:186648200-186651200	Active TSS	NH-A	brain
8	chr1:186648400-186652000	Active TSS	Right Atrium	heart
9	chr1:186648600-186651200	Active TSS	Hela-S3	cervix
10	chr1:186648600-186651400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:186648600-186651400	Active TSS	NHLF	lung
12	chr1:186648600-186651600	Active TSS	HMEC	breast
13	chr1:186648600-186651800	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:186648600-186652000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:186648600-186652000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:186648600-186652400	Active TSS	NHEK	skin
17	chr1:186649200-186651200	Active TSS	Aorta	Aorta
18	chr1:186649200-186652400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:186650200-186652200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:186650400-186651600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:186650400-186652000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:186650600-186651600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:186650600-186651800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:186650600-186652000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:186650600-186652200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:186650800-186651200	Active TSS	Fetal Intestine Large	intestine
27	chr1:186650800-186651600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:186650800-186652000	Flanking Active TSS	HUVEC	blood vessel
29	chr1:186650800-186652000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:186651000-186651200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr1:186651000-186651200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
32	chr1:186651000-186651200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr1:186651000-186651200	Flanking Active TSS	A549	lung
34	chr1:186651000-186651400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr1:186651000-186651400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:186651000-186651400	Weak transcription	Fetal Lung	lung
37	chr1:186651000-186652000	Flanking Active TSS	Osteobl	bone
38	chr1:186651000-186652600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:186651000-186653200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links