Variant report

Variant	rs12133496
Chromosome Location	chr1:224860443-224860444
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	chr1:224850263..224854124-chr1:224858225..224860779,3	MCF-7	breast:
2	chr1:224859647..224863135-chr1:224864370..224868600,5	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10458376	0.90[AFR][1000 genomes]
rs10495223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495224	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915692	0.81[CEU][hapmap]
rs12030079	0.80[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12030696	0.81[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12032349	0.86[ASW][hapmap];0.81[CEU][hapmap];0.97[LWK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs12041370	0.86[ASW][hapmap];0.81[CEU][hapmap];0.97[LWK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12046028	0.81[CEU][hapmap]
rs12118224	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12123347	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs12133529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12134264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12135077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145463	0.94[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1499281	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1499282	0.86[ASW][hapmap];0.97[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs16851528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17514252	0.81[CEU][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs17514370	0.90[AFR][1000 genomes]
rs17573714	0.81[CEU][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs1846501	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs298736	0.81[CEU][hapmap]
rs3738363	0.81[CEU][hapmap]
rs3738364	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738365	0.81[CEU][hapmap]
rs4564105	0.81[CEU][hapmap]
rs55744530	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56121354	0.86[AFR][1000 genomes]
rs56228106	0.86[AFR][1000 genomes]
rs56365526	0.90[AFR][1000 genomes]
rs57395227	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58158731	0.89[EUR][1000 genomes]
rs6426145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665737	0.90[AFR][1000 genomes]
rs6666840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666853	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6676444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722849	0.81[CEU][hapmap]
rs7513639	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7521221	0.81[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7525096	0.81[CEU][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs7537218	0.90[AFR][1000 genomes]
rs7547239	0.81[CEU][hapmap]
rs7549891	0.81[CEU][hapmap];0.87[LWK][hapmap];0.85[AFR][1000 genomes]
rs930323	0.81[CEU][hapmap]
rs9660759	0.81[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9660787	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9661696	0.81[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9661955	0.81[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9662179	0.86[ASW][hapmap];0.83[LWK][hapmap]
rs9662190	0.86[ASW][hapmap];0.81[CEU][hapmap];0.97[LWK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv21093	chr1:224860202-224861277	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12133496	CNIH4	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224832800-224869000	Weak transcription	Dnd41	blood
3	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:224851400-224863000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:224857000-224862600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:224857200-224860800	Weak transcription	Left Ventricle	heart
7	chr1:224857200-224860800	Weak transcription	Ovary	ovary
8	chr1:224857200-224869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:224857200-224869200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:224857400-224860600	Weak transcription	Fetal Heart	heart
11	chr1:224857400-224860600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:224857400-224860800	Weak transcription	Fetal Stomach	stomach
13	chr1:224857400-224860800	Weak transcription	Pancreas	Pancrea
14	chr1:224857400-224861000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:224858400-224871800	Weak transcription	NHLF	lung
16	chr1:224858400-224874200	Weak transcription	NH-A	brain
17	chr1:224858600-224860600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:224858600-224861800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:224859600-224871400	Weak transcription	NHDF-Ad	bronchial
20	chr1:224860200-224861800	Enhancers	Fetal Brain Male	brain

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