Variant report

Variant	rs7342395
Chromosome Location	chr12:104668544-104668545
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104668426..104670566-chr12:104680778..104683191,4	MCF-7	breast:
2	chr12:104668134..104671112-chr12:104674176..104678107,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257732	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10735392	0.83[JPT][hapmap]
rs10735393	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs10745995	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10745996	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10745997	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10745998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10778311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10778315	0.86[ASN][1000 genomes]
rs10778316	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]
rs10778317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778323	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs10861169	0.81[JPT][hapmap]
rs10861204	0.83[JPT][hapmap]
rs11111960	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs11111962	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111970	0.91[AFR][1000 genomes]
rs11111973	0.90[AFR][1000 genomes]
rs12303195	0.80[AMR][1000 genomes]
rs12368657	0.94[AFR][1000 genomes]
rs12424869	1.00[JPT][hapmap]
rs17035324	0.81[JPT][hapmap]
rs28534514	0.94[AFR][1000 genomes]
rs28626346	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34494070	0.81[AFR][1000 genomes]
rs4129598	0.81[JPT][hapmap]
rs4246264	0.81[JPT][hapmap]
rs4246267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246269	0.83[JPT][hapmap]
rs4246271	0.83[JPT][hapmap]
rs4254139	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329742	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4406890	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs4545635	0.81[JPT][hapmap]
rs4569072	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964260	0.81[JPT][hapmap]
rs4964288	0.83[JPT][hapmap]
rs4964728	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs4964735	0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4964752	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs4964753	0.91[AFR][1000 genomes]
rs4964761	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs4964779	0.83[JPT][hapmap]
rs6539138	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7136838	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137305	0.82[ASN][1000 genomes]
rs7138523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294997	0.90[JPT][hapmap]
rs7295751	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301631	0.91[JPT][hapmap]
rs7310505	0.85[GIH][hapmap]
rs7342321	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957725	0.89[CHB][hapmap]
rs7969435	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975161	0.81[JPT][hapmap]
rs9668964	0.87[ASN][1000 genomes]
rs9738677	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9739833	0.83[JPT][hapmap]

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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7342395	STON2	trans	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104652000-104669600	Weak transcription	Hela-S3	cervix
2	chr12:104652800-104673000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr12:104658200-104670000	Weak transcription	NHLF	lung
4	chr12:104658200-104670200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:104658200-104670200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:104658200-104672800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:104663600-104670000	Weak transcription	Brain Substantia Nigra	brain
8	chr12:104664600-104673200	Weak transcription	HSMM	muscle
9	chr12:104666400-104668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:104666400-104668600	Weak transcription	NHEK	skin
11	chr12:104667000-104669600	Weak transcription	Stomach Mucosa	stomach
12	chr12:104667200-104669400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:104667200-104670000	Weak transcription	K562	blood
14	chr12:104667400-104668600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:104667600-104669400	Enhancers	A549	lung
16	chr12:104667600-104679600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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