Variant report

Variant	rs689466
Chromosome Location	chr1:186650751-186650752
allele	A/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	chr1:186649009-186650813	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:186647362-186650832	PBDE	blood:	n/a	n/a
3	POLR2A	chr1:186648986-186650813	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:186650697-186651259	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:186647276-186650764	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:186648078-186651650	IMR90	lung:	n/a	n/a
7	POLR2A	chr1:186646993-186651195	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr1:186648991-186650805	A549	lung:	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	TBP	chr1:186648845-186652253	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:186648899-186650975	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:186647207-186651362	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
2	chr1:186650209..186651033-chr6:89789993..89790875,2	Hela-S3	cervix:

Variant related genes	Relation type
PTGS2	TF binding region
ENSG00000271931	Chromatin interaction
ENSG00000146278	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10489396	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs10489397	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs11808900	0.86[JPT][hapmap]
rs11810534	0.85[JPT][hapmap]
rs12723621	0.82[JPT][hapmap]
rs4140432	0.83[JPT][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs689466	PDC	cis	cerebellum	SCAN
rs689466	GLUL	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186646400-186651000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:186647000-186652000	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:186647600-186651000	Active TSS	A549	lung
4	chr1:186647800-186651800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:186648000-186651200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:186648000-186651600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:186648000-186651800	Active TSS	Colon Smooth Muscle	Colon
8	chr1:186648000-186651800	Active TSS	NHDF-Ad	bronchial
9	chr1:186648200-186651000	Active TSS	Fetal Stomach	stomach
10	chr1:186648200-186651000	Active TSS	Osteobl	bone
11	chr1:186648200-186651200	Active TSS	NH-A	brain
12	chr1:186648400-186650800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:186648400-186650800	Active TSS	Colonic Mucosa	Colon
14	chr1:186648400-186650800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
15	chr1:186648400-186651000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:186648400-186652000	Active TSS	Right Atrium	heart
17	chr1:186648600-186651000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:186648600-186651200	Active TSS	Hela-S3	cervix
19	chr1:186648600-186651400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:186648600-186651400	Active TSS	NHLF	lung
21	chr1:186648600-186651600	Active TSS	HMEC	breast
22	chr1:186648600-186651800	Active TSS	Rectal Smooth Muscle	rectum
23	chr1:186648600-186652000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:186648600-186652000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:186648600-186652400	Active TSS	NHEK	skin
26	chr1:186648800-186650800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:186648800-186650800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:186648800-186650800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:186648800-186650800	Active TSS	Duodenum Mucosa	Duodenum
30	chr1:186648800-186650800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
31	chr1:186649000-186650800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:186649000-186650800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr1:186649000-186650800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:186649000-186650800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:186649000-186650800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
36	chr1:186649000-186650800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:186649000-186650800	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:186649200-186651200	Active TSS	Aorta	Aorta
39	chr1:186649200-186652400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:186649400-186650800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
41	chr1:186649600-186650800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:186649800-186650800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr1:186650000-186650800	Active TSS	Brain Angular Gyrus	brain
44	chr1:186650200-186650800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr1:186650200-186650800	Active TSS	Fetal Muscle Trunk	muscle
46	chr1:186650200-186650800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:186650200-186651000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:186650200-186652200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:186650400-186650800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
50	chr1:186650400-186650800	Bivalent Enhancer	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links