Variant report

Variant	rs10400561
Chromosome Location	chr12:104640920-104640921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104640550..104643138-chr12:104680715..104683734,3	MCF-7	breast:
2	chr12:104640249..104641804-chr12:104684614..104686978,2	MCF-7	breast:
3	chr12:104639901..104642308-chr12:104681072..104683014,3	K562	blood:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10745994	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10861181	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111931	0.83[AFR][1000 genomes]
rs11111943	0.88[ASN][1000 genomes]
rs11111946	0.89[AFR][1000 genomes]
rs11111955	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12296767	0.84[AFR][1000 genomes]
rs12308914	0.86[AFR][1000 genomes]
rs12310731	0.89[AFR][1000 genomes]
rs12311576	0.81[AFR][1000 genomes]
rs12322184	0.83[AFR][1000 genomes]
rs12322245	0.84[AFR][1000 genomes]
rs17035324	0.81[ASN][1000 genomes]
rs4129598	0.81[ASN][1000 genomes]
rs4246264	0.88[ASN][1000 genomes]
rs4388968	0.82[ASN][1000 genomes]
rs4406890	0.96[EUR][1000 genomes]
rs4545635	0.88[ASN][1000 genomes]
rs4964257	0.88[ASN][1000 genomes]
rs4964260	0.88[ASN][1000 genomes]
rs4964267	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964270	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4964271	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964728	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61524019	0.83[AFR][1000 genomes]
rs6419386	0.80[ASN][1000 genomes]
rs6539128	0.81[ASN][1000 genomes]
rs6539132	0.89[EUR][1000 genomes]
rs7138317	0.83[ASN][1000 genomes]
rs7295413	0.80[ASN][1000 genomes]
rs7297560	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7305872	0.83[ASN][1000 genomes]
rs73392593	0.83[AFR][1000 genomes]
rs73394524	0.86[AFR][1000 genomes]
rs7958851	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7960443	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7975161	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978101	0.81[ASN][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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104638000-104642400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:104638000-104642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:104638200-104641000	Weak transcription	A549	lung

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