Variant report

Variant	rs12211425
Chromosome Location	chr6:133132500-133132501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:133132497-133132780	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:133132413-133132751	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr6:133132484-133132726	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr6:133132365-133132815	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:133132464-133132742	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr6:133132429-133132761	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:133132359-133132876	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr6:133132428-133132868	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr6:133132394-133132790	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr6:133132481-133132781	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr6:133132380-133132996	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133118544..133124606-chr6:133132137..133138834,13	MCF-7	breast:

Variant related genes	Relation type
RPS12	TF binding region
SNORD101	TF binding region
ENSG00000146409	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10457591	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10457593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457595	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457596	0.85[CEU][hapmap]
rs10484628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073512	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs11154698	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128998	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758796	0.81[ASN][1000 genomes]
rs11965044	0.94[YRI][hapmap]
rs12190684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191058	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193474	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12194625	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12194802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195249	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196336	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198970	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12199381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12200848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201540	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201769	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12202407	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203738	0.92[ASN][1000 genomes]
rs12204027	1.00[CHB][hapmap]
rs12204693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212934	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215084	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215088	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215486	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061741	0.89[LWK][hapmap];0.95[YRI][hapmap]
rs17061751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143387	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294761	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28693848	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706652	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778175	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813347	1.00[JPT][hapmap]
rs55708537	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959738	0.85[ASN][1000 genomes]
rs56170227	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58265543	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59543333	0.81[EUR][1000 genomes]
rs60062075	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60412119	0.85[ASN][1000 genomes]
rs62425110	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425114	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425132	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425133	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425137	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426668	0.81[ASN][1000 genomes]
rs62426674	0.81[ASN][1000 genomes]
rs6934161	1.00[CHB][hapmap]
rs73772960	0.80[AFR][1000 genomes]
rs7760377	0.95[YRI][hapmap]
rs7770641	0.85[ASW][hapmap];0.89[LWK][hapmap];0.95[YRI][hapmap]
rs9375919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389033	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402452	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402453	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9493445	1.00[CHB][hapmap]
rs9493446	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12211425	C6orf192	Cis_1M	lymphoblastoid	RTeQTL
rs12211425	C6orf192	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133120800-133134000	Weak transcription	Pancreas	Pancrea
2	chr6:133121200-133133600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:133130000-133133600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:133131200-133133200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:133131600-133133600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:133131800-133133400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:133132200-133132800	Enhancers	K562	blood
8	chr6:133132200-133133000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:133132200-133133600	Enhancers	Adipose Nuclei	Adipose
10	chr6:133132400-133132800	Enhancers	Fetal Lung	lung
11	chr6:133132400-133133200	Enhancers	Liver	Liver
12	chr6:133132400-133133400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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