Variant report

Variant	rs3847967
Chromosome Location	chr12:120722064-120722065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120690051..120707499-chr12:120720410..120732530,91	MCF-7	breast:
2	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
3	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
4	chr12:120626707..120642605-chr12:120719450..120732919,96	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089154	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000240925	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1151826	0.89[CHB][hapmap]
rs1151828	0.89[CHB][hapmap]
rs1151835	0.89[CHB][hapmap]
rs1151836	0.89[CHB][hapmap]
rs1179386	0.89[CHB][hapmap]
rs12299143	0.81[EUR][1000 genomes]
rs12423303	0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap]
rs12424233	1.00[CEU][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12424555	0.86[EUR][1000 genomes]
rs12425936	0.92[JPT][hapmap]
rs12426368	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12426900	0.92[JPT][hapmap]
rs12427095	0.91[JPT][hapmap]
rs1634820	0.89[CHB][hapmap]
rs16950044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16950047	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16950058	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs16950061	0.81[EUR][1000 genomes]
rs16950065	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs16950101	0.81[EUR][1000 genomes]
rs2238161	0.81[EUR][1000 genomes]
rs2239207	0.89[CHB][hapmap]
rs2464296	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2701641	0.89[CHB][hapmap]
rs3847968	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3847969	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3898618	0.81[EUR][1000 genomes]
rs5634	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs57279831	0.81[EUR][1000 genomes]
rs57384430	0.82[EUR][1000 genomes]
rs59768240	0.81[EUR][1000 genomes]
rs61140476	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61665022	0.86[EUR][1000 genomes]
rs61748115	0.84[EUR][1000 genomes]
rs7311566	0.84[JPT][hapmap]
rs7960401	0.81[EUR][1000 genomes]
rs9657936	1.00[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs9657941	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9657942	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9657948	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
5	nsv560435	chr12:120695141-120769657	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
6	nsv899556	chr12:120695141-120779931	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3847967	SIRT4	cis	multi-tissue	Pritchard
rs3847967	SIRT4	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120716800-120728600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:120717400-120724600	Weak transcription	A549	lung
3	chr12:120717400-120728600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:120718400-120722400	Enhancers	Placenta	Placenta
5	chr12:120720400-120724000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:120720400-120724200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:120720400-120725000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:120721400-120724200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:120721400-120724600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:120721600-120723400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:120721600-120728600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:120721800-120722400	Weak transcription	K562	blood
13	chr12:120721800-120724000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:120722000-120722200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:120722000-120722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:120722000-120722400	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links