Variant report

Variant	rs6462054
Chromosome Location	chr7:27886171-27886172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10486564	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12154292	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12700846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17156032	1.00[EUR][1000 genomes]
rs1859328	0.80[ASN][1000 genomes]
rs199	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2237345	0.82[AMR][1000 genomes]
rs720660	1.00[AFR][1000 genomes];1.00[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1018550	chr7:27844038-27925645	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6462054	PTGS2	trans	brain	seeQTL
rs6462054	GADD45G	trans	brain	seeQTL
rs6462054	FOSB	trans	brain	seeQTL
rs6462054	CCL4	trans	brain	seeQTL
rs6462054	CCDC109B	trans	brain	seeQTL
rs6462054	RGS2	trans	brain	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27870600-27891800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:27871400-27889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:27872800-27890000	Weak transcription	Fetal Lung	lung
4	chr7:27873800-27886200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:27874400-27888600	Weak transcription	Brain Angular Gyrus	brain
6	chr7:27875200-27913000	Weak transcription	Right Atrium	heart
7	chr7:27876200-27913000	Weak transcription	Fetal Heart	heart
8	chr7:27876400-27886200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:27880000-27891600	Weak transcription	Osteobl	bone
10	chr7:27880400-27891000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:27880600-27889000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:27880600-27903000	Weak transcription	Lung	lung
13	chr7:27880600-27913600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:27880800-27895600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:27880800-27896600	Weak transcription	Spleen	Spleen
16	chr7:27880800-27896800	Weak transcription	Gastric	stomach
17	chr7:27880800-27913200	Weak transcription	Aorta	Aorta
18	chr7:27881000-27905600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:27881200-27895800	Weak transcription	Primary T cells from cord blood	blood
20	chr7:27881600-27895600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:27881800-27896600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:27882600-27895400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:27882800-27886600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:27882800-27888800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:27882800-27912000	Weak transcription	Brain Anterior Caudate	brain
26	chr7:27883600-27896000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:27883600-27903000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:27883800-27892000	Weak transcription	Fetal Stomach	stomach
29	chr7:27883800-27903000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:27884600-27895800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:27885200-27900400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:27885600-27886400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:27885800-27886400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr7:27886000-27886800	Enhancers	HMEC	breast
35	chr7:27886000-27887000	Enhancers	NHEK	skin
36	chr7:27886000-27887200	Strong transcription	Primary B cells from cord blood	blood

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