Variant report

Variant	rs58866635
Chromosome Location	chr15:34315910-34315911
allele	A/G
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: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12050519	1.00[EUR][1000 genomes]
rs12050691	0.97[EUR][1000 genomes]
rs12050692	0.96[EUR][1000 genomes]
rs1424399	1.00[EUR][1000 genomes]
rs16958595	1.00[ASN][1000 genomes]
rs2018672	1.00[EUR][1000 genomes]
rs2879446	0.99[EUR][1000 genomes]
rs4542632	0.99[EUR][1000 genomes]
rs563895	1.00[EUR][1000 genomes]
rs56743146	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57987098	0.90[ASN][1000 genomes]
rs58113983	0.99[EUR][1000 genomes]
rs59031451	0.99[EUR][1000 genomes]
rs59502570	0.86[ASN][1000 genomes]
rs60757549	0.86[ASN][1000 genomes]
rs60880416	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61153924	0.98[ASN][1000 genomes]
rs61196776	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67436900	1.00[EUR][1000 genomes]
rs7165892	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168444	0.99[EUR][1000 genomes]
rs7170890	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7182790	1.00[EUR][1000 genomes]
rs73387944	0.99[EUR][1000 genomes]
rs7494836	0.86[ASN][1000 genomes]
rs991755	1.00[EUR][1000 genomes]
rs994849	1.00[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58866635	CHRM5	cis	Nerve Tibial	GTEx

Chromatin state (count:16 , 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	chr15:34309400-34316000	Weak transcription	Brain Angular Gyrus	brain
4	chr15:34309400-34330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:34309600-34330000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:34311000-34318600	Weak transcription	Primary T cells from cord blood	blood
7	chr15:34314200-34326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:34314400-34316400	Enhancers	Brain Substantia Nigra	brain
9	chr15:34315200-34317200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:34315400-34316000	Enhancers	Esophagus	oesophagus
11	chr15:34315600-34316400	Enhancers	HepG2	liver
12	chr15:34315800-34316400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:34315800-34316400	Enhancers	Brain Cingulate Gyrus	brain
14	chr15:34315800-34316400	Enhancers	Stomach Mucosa	stomach
15	chr15:34315800-34316600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:34315800-34316600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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