Variant report

Variant	rs12108246
Chromosome Location	chr4:54078164-54078165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10517291	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs10517292	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs11133246	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11133247	0.91[ASN][1000 genomes]
rs11929903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11939189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947928	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12499016	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12499731	0.82[AMR][1000 genomes]
rs12500564	0.82[AMR][1000 genomes]
rs12503963	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505661	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12507228	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512359	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12512748	0.85[AMR][1000 genomes]
rs12640471	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12646150	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647441	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12650397	0.90[ASN][1000 genomes]
rs17082453	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17082476	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17082504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082529	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082549	0.85[AMR][1000 genomes]
rs17082565	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs1987028	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2001881	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs2128103	0.83[CHD][hapmap]
rs34019927	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4299650	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4419530	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4421047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4515221	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4529117	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864451	0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4864452	0.85[AMR][1000 genomes]
rs4864453	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs4864454	0.85[AMR][1000 genomes]
rs4864747	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs6826467	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs6830879	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6854446	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73143456	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73143458	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73143484	0.91[ASN][1000 genomes]
rs73147378	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73147396	0.82[AMR][1000 genomes]
rs73149212	0.80[AMR][1000 genomes]
rs751265	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs7687029	0.85[AMR][1000 genomes]
rs7688646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7696426	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9761301	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9762074	0.85[AMR][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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv17516	chr4:54069503-54079714	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
4	esv2421791	chr4:54070961-54080242	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
5	nsv441876	chr4:54070961-54080242	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	nsv514213	chr4:54073451-54079819	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12108246	SPINK2	cis	cerebellum	SCAN
rs12108246	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
2	chr4:54053000-54093000	Weak transcription	Primary B cells from cord blood	blood
3	chr4:54058200-54079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:54063400-54079400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:54064400-54078400	Weak transcription	Small Intestine	intestine
6	chr4:54064400-54106600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:54066200-54080000	Weak transcription	Psoas Muscle	Psoas
8	chr4:54066400-54099000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:54072600-54085000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:54072800-54089000	Weak transcription	NHDF-Ad	bronchial
11	chr4:54073400-54079200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:54076800-54088200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:54077800-54107600	Weak transcription	Lung	lung
14	chr4:54078000-54089600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:54078000-54107200	Weak transcription	Primary T cells from cord blood	blood

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