Variant report

Variant	rs11608602
Chromosome Location	chr12:44215732-44215733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:44214138..44217939-chr12:44227054..44230116,3	K562	blood:
2	chr12:44207357..44209830-chr12:44214435..44216907,3	K562	blood:
3	chr12:44215623..44218391-chr12:44230316..44232380,2	K562	blood:
4	chr12:44195581..44201373-chr12:44212394..44217979,6	K562	blood:
5	chr12:44214277..44216042-chr12:44228504..44230810,2	MCF-7	breast:
6	chr12:44203831..44205856-chr12:44214140..44216950,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction
ENSG00000151239	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10880569	0.90[ASN][1000 genomes]
rs10880570	1.00[CHB][hapmap];0.86[GIH][hapmap];0.90[ASN][1000 genomes]
rs10880574	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs11182268	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11182269	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs11182270	0.84[ASN][1000 genomes]
rs11182279	0.84[ASN][1000 genomes]
rs11182281	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11182282	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11182284	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182286	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11182287	0.89[ASN][1000 genomes]
rs11182288	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182289	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11182291	0.85[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs11556066	0.84[ASN][1000 genomes]
rs11835197	0.88[MEX][hapmap]
rs11837742	0.86[MEX][hapmap]
rs12226960	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12228995	0.87[ASN][1000 genomes]
rs12230695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231553	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12829856	0.84[ASN][1000 genomes]
rs1531402	0.85[MEX][hapmap]
rs1816854	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28437935	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35980560	0.84[ASN][1000 genomes]
rs61290421	0.81[ASN][1000 genomes]
rs73093785	0.84[ASN][1000 genomes]
rs7966902	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11608602	ARID2	cis	parietal	SCAN
rs11608602	GXYLT1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44202000-44217800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:44208400-44223600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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