Variant report

Variant	rs11172541
Chromosome Location	chr12:39942758-39942759
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	chr12:39932301..39934911-chr12:39941058..39943414,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf40-1	chr12:39942705-39943943	NONHSAT027707

Variant related genes	Relation type
ENSG00000270273	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10876886	0.95[JPT][hapmap]
rs10876972	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs10876989	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877100	0.91[ASN][1000 genomes]
rs11171891	0.91[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11171901	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11171923	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs11171938	0.95[CEU][hapmap]
rs11172108	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs11172120	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11172183	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11172235	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172264	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172282	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172319	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172320	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172357	0.87[ASN][1000 genomes]
rs11172386	0.87[ASN][1000 genomes]
rs11172392	0.87[ASN][1000 genomes]
rs11172492	0.84[CEU][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11172493	0.89[ASN][1000 genomes]
rs11172526	0.87[ASN][1000 genomes]
rs11172592	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172625	0.89[ASN][1000 genomes]
rs11172638	0.89[ASN][1000 genomes]
rs11172650	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172661	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11830643	0.95[JPT][hapmap]
rs12228767	0.95[JPT][hapmap]
rs12230604	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12424345	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs1512936	0.95[JPT][hapmap]
rs1567739	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs1828653	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2388320	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs3736466	0.91[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4284427	0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4320988	0.84[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4378431	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4390378	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4451772	0.84[ASN][1000 genomes]
rs4466883	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4475956	0.83[ASN][1000 genomes]
rs4492858	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs4500523	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4564382	0.87[EUR][1000 genomes]
rs59695906	0.90[EUR][1000 genomes]
rs60263267	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60900225	0.90[EUR][1000 genomes]
rs6581187	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581188	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137143	0.91[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs73096532	0.87[ASN][1000 genomes]
rs7316073	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7485730	0.89[ASN][1000 genomes]
rs7962283	0.83[CEU][hapmap]
rs7964447	0.95[JPT][hapmap]
rs7966540	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7968837	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7974928	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7979444	0.95[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1048933	chr12:39886665-39946270	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39935400-39946400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr12:39936000-39945800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:39938800-39951000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:39939800-39950800	Weak transcription	Primary T cells from cord blood	blood
5	chr12:39941400-39949600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:39942600-39951600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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