Variant report

Variant	rs12230710
Chromosome Location	chr12:40527897-40527898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40526853..40529105-chr12:40530805..40532717,2	MCF-7	breast:
2	12:40525880-40532672..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1031996	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10784370	0.80[EUR][1000 genomes]
rs10784381	0.84[EUR][1000 genomes]
rs10784386	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10784387	0.85[ASN][1000 genomes]
rs10878113	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1117378	0.82[EUR][1000 genomes]
rs11175275	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11175326	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11175327	0.81[ASN][1000 genomes]
rs1388590	0.81[ASN][1000 genomes]
rs1472118	0.80[EUR][1000 genomes]
rs1482284	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1482285	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1482287	0.82[EUR][1000 genomes]
rs1482288	0.82[EUR][1000 genomes]
rs1491931	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1905121	0.82[EUR][1000 genomes]
rs2170503	0.84[EUR][1000 genomes]
rs2404573	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2638231	0.82[EUR][1000 genomes]
rs2638232	0.82[EUR][1000 genomes]
rs2638260	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638262	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638263	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638264	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638266	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708449	0.82[EUR][1000 genomes]
rs3812791	0.82[EUR][1000 genomes]
rs6581514	0.81[EUR][1000 genomes]
rs6581519	0.82[EUR][1000 genomes]
rs7132203	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs729216	0.82[EUR][1000 genomes]
rs7306140	0.81[EUR][1000 genomes]
rs7310430	0.81[EUR][1000 genomes]
rs878010	0.82[EUR][1000 genomes]
rs900253	0.82[EUR][1000 genomes]
rs937109	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937110	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937111	0.82[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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12230710	AC079630.2	cis	Esophagus Mucosa	GTEx
rs12230710	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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