Variant report

Variant	rs7197485
Chromosome Location	chr16:46910519-46910520
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	chr16:46910117..46912387-chr16:46912466..46915411,3	MCF-7	breast:
2	chr16:46910161..46915169-chr16:46917028..46920503,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166123	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1009391	0.86[CEU][hapmap];0.90[GIH][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.90[GIH][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12931259	0.81[AFR][1000 genomes]
rs12934580	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935606	0.87[EUR][1000 genomes]
rs1641122	1.00[ASN][1000 genomes]
rs1651654	0.90[GIH][hapmap]
rs16948661	0.90[GIH][hapmap]
rs17189741	0.81[GIH][hapmap]
rs1869006	0.93[CEU][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3218744	1.00[CHB][hapmap]
rs35354454	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36481	0.90[GIH][hapmap]
rs4246381	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401068	0.81[GIH][hapmap]
rs4966706	0.86[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	0.88[GIH][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.90[GIH][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.84[ASW][hapmap];0.90[GIH][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	0.89[ASW][hapmap];0.90[GIH][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.87[EUR][1000 genomes]
rs56042735	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.86[EUR][1000 genomes]
rs57127559	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	1.00[ASN][1000 genomes]
rs58074838	0.84[EUR][1000 genomes]
rs59708508	0.83[EUR][1000 genomes]
rs62057633	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	1.00[ASN][1000 genomes]
rs7186748	0.87[EUR][1000 genomes]
rs7187475	0.90[GIH][hapmap]
rs7192574	0.83[EUR][1000 genomes]
rs7196375	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.90[GIH][hapmap]
rs72812428	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734309	0.83[ASW][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs8044443	0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs8051017	0.90[GIH][hapmap]
rs8053137	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	1.00[ASN][1000 genomes]
rs8058734	1.00[ASN][1000 genomes]
rs808432	0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs808783	0.81[GIH][hapmap]
rs9328668	0.89[ASW][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1831215	chr16:46907546-46962858	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7197485	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs7197485	MYLK3	cis	cerebellum	SCAN
rs7197485	LONP2	cis	cerebellum	SCAN
rs7197485	SHCBP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46888400-46913400	Weak transcription	Esophagus	oesophagus
2	chr16:46903200-46911200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr16:46905600-46914400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:46909800-46911000	Enhancers	Fetal Lung	lung
5	chr16:46909800-46911600	Enhancers	Liver	Liver
6	chr16:46910000-46910600	Enhancers	Ovary	ovary
7	chr16:46910000-46910800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:46910000-46910800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr16:46910000-46911200	Weak transcription	Pancreas	Pancrea
10	chr16:46910200-46910600	Enhancers	Adipose Nuclei	Adipose
11	chr16:46910200-46910800	Flanking Active TSS	HepG2	liver
12	chr16:46910200-46911600	Enhancers	Stomach Mucosa	stomach
13	chr16:46910400-46910800	Enhancers	Fetal Kidney	kidney
14	chr16:46910400-46910800	Flanking Active TSS	A549	lung

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