Variant report

Variant	rs6550227
Chromosome Location	chr3:19976253-19976254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19976162..19983592-chr3:19985528..19991017,8	MCF-7	breast:
2	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12638170	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2171275	0.85[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs2364515	0.82[CHD][hapmap]
rs2929318	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929319	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929343	0.85[CHD][hapmap]
rs2929345	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2929346	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929347	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929349	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2929350	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2929351	0.88[ASN][1000 genomes]
rs2929353	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929354	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929355	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929356	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929357	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929359	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2929360	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs2929366	0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs2931403	0.80[JPT][hapmap]
rs2931407	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57808479	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770750	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6550227	EFHB,LOC100130288	cis	occipital cortex	BrainEAC
rs6550227	SGOL1	cis	parietal	SCAN
rs6550227	EFHB,LOC100130288	cis	substantia nigra	BrainEAC
rs6550227	EFHB,LOC100130288	cis	thalamus	BrainEAC
rs6550227	EFHB,LOC100130288	cis	putamen	BrainEAC
rs6550227	EFHB,LOC100130288	cis	intralobular white matter	BrainEAC
rs6550227	EFHB,LOC100130288	cis	temporal cortex	BrainEAC
rs6550227	UBE2E2	cis	cerebellum	SCAN
rs6550227	KCNMA1	trans	lymphoblastoid	seeQTL
rs6550227	EFHB,LOC100130288	cis	hippocampus	BrainEAC
rs6550227	EFHB,LOC100130288	cis	frontal cortex	BrainEAC
rs6550227	EFHB,LOC100130288	cis	brain	BrainEAC

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19973600-19979200	Weak transcription	HMEC	breast
2	chr3:19973600-19987200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:19973800-19978400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:19973800-19979000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:19974200-19979200	Weak transcription	Hela-S3	cervix
6	chr3:19975000-19976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:19975200-19976400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:19975200-19976400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr3:19975600-19987400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:19976000-19976800	Enhancers	K562	blood
11	chr3:19976000-19979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:19976000-19979200	Weak transcription	HepG2	liver
13	chr3:19976000-19987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:19976200-19979000	Weak transcription	A549	lung

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