Variant report

Variant	rs1156727
Chromosome Location	chr12:74039243-74039244
allele	A/C
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	CTCF	chr12:74039140-74039290	GM12868	blood:	n/a	n/a
2	POLR2A	chr12:74039137-74039325	MCF-7	breast:	n/a	n/a
3	MYC	chr12:74039162-74039261	MCF-7	breast:	n/a	n/a
4	POLR2A	chr12:74039060-74039342	MCF-7	breast:	n/a	n/a
5	POLR2A	chr12:74039106-74039304	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000243164	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1156726	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1595791	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1867331	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867333	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2083398	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2083855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099936	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218155	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2244515	0.82[EUR][1000 genomes]
rs2264880	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2264881	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2580959	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586917	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586919	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586922	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2586923	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586925	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2586926	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586927	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586937	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2730528	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2731579	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs981632	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1043656	chr12:73795943-74341905	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv541536	chr12:73795943-74341905	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832458	chr12:73885329-74075491	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1037030	chr12:73898311-74656764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541537	chr12:73898311-74656764	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1039792	chr12:73932372-74092387	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1054215	chr12:73955467-74080646	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899279	chr12:74010790-74072269	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1040846	chr12:74033679-74295583	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv541538	chr12:74033679-74295583	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1156727	GLIPR1L1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74038400-74041200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:74038600-74040600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:74039000-74039800	ZNF genes & repeats	Brain Hippocampus Middle	brain
4	chr12:74039200-74039400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:74039200-74040400	ZNF genes & repeats	Liver	Liver

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