Variant report

Variant	rs4246260
Chromosome Location	chr12:104570969-104570970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104530177..104533540-chr12:104569302..104573926,9	MCF-7	breast:
2	chr12:104570809..104571731-chr12:104687793..104688584,2	MCF-7	breast:
3	chr12:104564791..104567133-chr12:104568799..104572664,3	K562	blood:
4	chr12:104570742..104573318-chr12:104574956..104577002,2	K562	blood:
5	chr12:104528363..104533397-chr12:104570131..104576145,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11111916	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap];0.93[ASN][1000 genomes]
rs11111917	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11111940	0.87[CEU][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs11613944	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11829709	0.90[ASN][1000 genomes]
rs11836726	0.87[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs4246261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4321026	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4371000	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4445711	0.82[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs4522249	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964626	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964628	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964678	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61939220	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6539125	0.82[JPT][hapmap]
rs7297296	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7297956	0.87[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs7957744	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958262	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs7961381	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966970	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969538	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972172	0.82[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975524	0.87[CEU][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9668556	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9705582	0.89[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	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4246260	EID3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104566400-104573400	Weak transcription	Spleen	Spleen
2	chr12:104567000-104571000	Weak transcription	K562	blood
3	chr12:104570000-104571000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:104570000-104573000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:104570400-104571000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:104570600-104571000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:104570600-104571000	Enhancers	Hela-S3	cervix
8	chr12:104570600-104571200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:104570800-104572400	Flanking Active TSS	A549	lung
10	chr12:104570800-104572600	Enhancers	NHLF	lung
11	chr12:104570800-104572800	Enhancers	Rectal Smooth Muscle	rectum

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