Variant report

Variant	rs12372231
Chromosome Location	chr12:121351729-121351730
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	chr12:121342121..121344461-chr12:121350958..121352582,2	K562	blood:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10774572	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849807	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065300	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065307	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065311	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11065324	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065332	0.92[ASN][1000 genomes]
rs1151849	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1151859	0.88[ASN][1000 genomes]
rs1151862	0.88[ASN][1000 genomes]
rs1168944	0.89[ASN][1000 genomes]
rs1168946	0.89[ASN][1000 genomes]
rs1168948	0.89[ASN][1000 genomes]
rs1168953	0.89[ASN][1000 genomes]
rs1177585	0.89[ASN][1000 genomes]
rs1179939	0.89[ASN][1000 genomes]
rs12371178	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12580949	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12809299	0.80[EUR][1000 genomes]
rs12822123	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12831094	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1542859	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1696357	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696390	0.96[ASN][1000 genomes]
rs1718188	0.97[ASN][1000 genomes]
rs2393716	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2650017	0.89[ASN][1000 genomes]
rs2701177	0.97[ASN][1000 genomes]
rs2701184	0.99[ASN][1000 genomes]
rs34009825	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35905305	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809313	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3897746	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4454799	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4766980	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4767941	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs487943	0.85[ASN][1000 genomes]
rs520753	0.85[ASN][1000 genomes]
rs533264	0.85[ASN][1000 genomes]
rs548452	0.84[ASN][1000 genomes]
rs58918988	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs602984	0.85[ASN][1000 genomes]
rs609700	0.85[ASN][1000 genomes]
rs610694	0.85[ASN][1000 genomes]
rs61946382	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61946383	0.97[ASN][1000 genomes]
rs61946384	0.98[ASN][1000 genomes]
rs61946385	0.97[ASN][1000 genomes]
rs61946386	0.97[ASN][1000 genomes]
rs647881	0.85[ASN][1000 genomes]
rs665585	0.84[ASN][1000 genomes]
rs666976	0.82[ASN][1000 genomes]
rs73413868	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73415720	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73415734	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967190	0.92[ASN][1000 genomes]
rs7969140	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7980311	0.99[ASN][1000 genomes]
rs869781	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs904628	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv560448	chr12:121341477-121364324	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv560452	chr12:121341581-121357934	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv560453	chr12:121342186-121364324	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv975534	chr12:121347729-121360386	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12372231	SPPL3	cis	Nerve Tibial	GTEx
rs12372231	ACADS	cis	Thyroid	GTEx
rs12372231	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121343000-121362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:121346000-121352200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:121347400-121352200	Weak transcription	Esophagus	oesophagus
4	chr12:121347600-121352200	Weak transcription	Placenta	Placenta
5	chr12:121348000-121352200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links