Variant report

Variant	rs2702282
Chromosome Location	chr15:34316062-34316063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34314534..34316475-chr15:34330485..34333173,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169857	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11856529	0.84[EUR][1000 genomes]
rs1872806	0.99[ASN][1000 genomes]
rs2078561	0.97[ASN][1000 genomes]
rs2078562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2243858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2339351	0.86[ASN][1000 genomes]
rs2632075	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2632076	1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2632078	0.99[ASN][1000 genomes]
rs2632079	0.99[ASN][1000 genomes]
rs2632107	0.99[ASN][1000 genomes]
rs2684931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2684932	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2684933	0.85[ASN][1000 genomes]
rs2684939	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2684941	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2684943	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2684956	0.94[ASN][1000 genomes]
rs2684958	0.91[ASN][1000 genomes]
rs2702278	0.97[ASN][1000 genomes]
rs2702281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2702285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2702306	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28870091	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs478125	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs481391	0.84[ASN][1000 genomes]
rs489832	0.84[ASW][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5016373	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511422	0.84[ASW][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs543621	0.84[ASN][1000 genomes]
rs544114	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55805034	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs563663	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs569035	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs588655	0.84[ASW][hapmap]
rs602807	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs603152	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs604041	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs613479	0.84[ASN][1000 genomes]
rs625596	0.84[ASN][1000 genomes]
rs635531	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs636842	0.84[ASW][hapmap]
rs644585	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs646950	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs6495421	0.84[EUR][1000 genomes]
rs6495422	0.84[EUR][1000 genomes]
rs6495423	0.84[EUR][1000 genomes]
rs6495424	0.84[EUR][1000 genomes]
rs6495425	0.84[EUR][1000 genomes]
rs6495426	0.84[EUR][1000 genomes]
rs6495459	0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs682052	0.85[ASN][1000 genomes]
rs718690	0.85[ASN][1000 genomes]
rs8030334	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs8038713	0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs8040776	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	29 gene(s)	inside rSNPs	diseases
4	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2702282	CHRM5	cis	cerebellum	SCAN
rs2702282	AVEN	cis	lymphoblastoid	seeQTL
rs2702282	CHRM5	cis	parietal	SCAN
rs2702282	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34304200-34319800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:34309000-34317400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:34309400-34330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:34309600-34330000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:34311000-34318600	Weak transcription	Primary T cells from cord blood	blood
6	chr15:34314200-34326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:34314400-34316400	Enhancers	Brain Substantia Nigra	brain
8	chr15:34315200-34317200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:34315600-34316400	Enhancers	HepG2	liver
10	chr15:34315800-34316400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:34315800-34316400	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:34315800-34316400	Enhancers	Stomach Mucosa	stomach
13	chr15:34315800-34316600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:34315800-34316600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:34316000-34316200	Enhancers	Brain Angular Gyrus	brain

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