Variant report

Variant	rs336544
Chromosome Location	chr3:161060558-161060559
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161001819..161012846-chr3:161052557..161065154,32	MCF-7	breast:
2	chr3:161042109..161044562-chr3:161058166..161061121,3	MCF-7	breast:
3	chr3:160990337..160994329-chr3:161056046..161062548,7	MCF-7	breast:
4	chr3:161016283..161019052-chr3:161060342..161062317,2	MCF-7	breast:
5	chr3:161032948..161035717-chr3:161058882..161060875,3	MCF-7	breast:
6	chr3:160939100..160942199-chr3:161058343..161060677,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000240138	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12488318	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494261	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494844	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs13318781	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs1450519	0.83[CHB][hapmap]
rs1471440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1478567	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs163138	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs336564	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336565	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs336571	0.93[ASN][1000 genomes]
rs336573	0.94[ASN][1000 genomes]
rs336574	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs336576	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs336581	0.93[ASN][1000 genomes]
rs336584	0.93[ASN][1000 genomes]
rs336587	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336588	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336592	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs419703	0.90[ASN][1000 genomes]
rs4429651	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4487256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4490410	0.94[CHB][hapmap]
rs455739	0.91[ASN][1000 genomes]
rs458197	0.91[ASN][1000 genomes]
rs459067	0.91[ASN][1000 genomes]
rs461616	0.91[ASN][1000 genomes]
rs462081	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57201455	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278055	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62279860	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62279861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62279862	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62279892	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73160362	0.85[ASN][1000 genomes]
rs73162530	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9290072	0.87[CHB][hapmap]
rs9290075	0.92[ASN][1000 genomes]
rs978933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9812083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9825118	0.94[CHB][hapmap];0.91[YRI][hapmap]
rs9827833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9828189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9828231	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9831725	0.83[ASN][1000 genomes]
rs9836094	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859045	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876553	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
5	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs336544	DHX33	trans	brain	seeQTL
rs336544	RANBP10	trans	brain	seeQTL
rs336544	RAPGEF6	trans	brain	seeQTL
rs336544	ADCK3	trans	brain	seeQTL
rs336544	HELZ	trans	brain	seeQTL
rs336544	ANKRD10	trans	brain	seeQTL
rs336544	MICAL3	trans	brain	seeQTL
rs336544	ZNF337	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161051800-161061800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:161054000-161062600	Enhancers	HepG2	liver
3	chr3:161058200-161072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:161058400-161067000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:161059200-161064400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:161060000-161060600	Enhancers	Esophagus	oesophagus

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