Variant report

Variant	rs12154723
Chromosome Location	chr7:98036628-98036629
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98028827..98031634-chr7:98036336..98039927,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006453	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1076272	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808107	0.85[EUR][1000 genomes]
rs10953256	0.85[EUR][1000 genomes]
rs10953257	0.86[EUR][1000 genomes]
rs10953261	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11496115	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11761206	0.84[EUR][1000 genomes]
rs11765794	0.86[EUR][1000 genomes]
rs12112351	0.82[EUR][1000 genomes]
rs12667634	0.86[EUR][1000 genomes]
rs12672092	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12673586	0.81[EUR][1000 genomes]
rs12704988	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12704989	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232181	0.82[EUR][1000 genomes]
rs13237102	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13245076	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13246843	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13246868	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13307593	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1468338	0.85[EUR][1000 genomes]
rs1468340	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1468341	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1859482	0.86[EUR][1000 genomes]
rs2107716	0.83[EUR][1000 genomes]
rs2158553	0.84[EUR][1000 genomes]
rs2240349	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2286074	0.85[EUR][1000 genomes]
rs2394852	0.83[EUR][1000 genomes]
rs2394854	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34717219	0.86[EUR][1000 genomes]
rs34835415	0.86[EUR][1000 genomes]
rs35535338	0.86[EUR][1000 genomes]
rs35997266	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs36017146	0.86[EUR][1000 genomes]
rs36099592	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3779193	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779194	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3801251	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801254	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3801255	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801256	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801257	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801263	0.86[EUR][1000 genomes]
rs3801264	0.85[EUR][1000 genomes]
rs3823740	0.85[EUR][1000 genomes]
rs55825602	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56286037	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60077733	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62478174	0.80[EUR][1000 genomes]
rs62478175	0.84[EUR][1000 genomes]
rs62478200	0.86[EUR][1000 genomes]
rs62478203	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62478233	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62478236	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62478237	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465666	0.82[EUR][1000 genomes]
rs6465667	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6465669	0.82[EUR][1000 genomes]
rs6465670	0.82[EUR][1000 genomes]
rs6465671	0.85[EUR][1000 genomes]
rs6465672	0.86[EUR][1000 genomes]
rs6465673	0.84[EUR][1000 genomes]
rs6465675	0.86[EUR][1000 genomes]
rs6465677	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6465678	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6465680	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6465681	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465682	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465683	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67132564	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944262	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6945554	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6948346	0.82[EUR][1000 genomes]
rs6948540	0.86[EUR][1000 genomes]
rs6949214	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6955647	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6956686	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6959506	0.86[EUR][1000 genomes]
rs6961129	0.86[EUR][1000 genomes]
rs6961438	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6961790	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6963210	0.85[EUR][1000 genomes]
rs6967576	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6967934	0.82[EUR][1000 genomes]
rs6968321	0.86[EUR][1000 genomes]
rs6969234	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6971825	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6973775	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6974943	0.86[EUR][1000 genomes]
rs6979373	0.86[EUR][1000 genomes]
rs71563562	0.84[EUR][1000 genomes]
rs7458551	0.85[EUR][1000 genomes]
rs7776638	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7777415	0.85[EUR][1000 genomes]
rs7787009	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7787418	0.86[EUR][1000 genomes]
rs7787858	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7789380	0.85[EUR][1000 genomes]
rs7791321	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7795176	0.86[EUR][1000 genomes]
rs7797943	0.85[EUR][1000 genomes]
rs7801992	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7803372	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7805267	0.84[EUR][1000 genomes]
rs7806524	0.84[AMR][1000 genomes]
rs7806739	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7807455	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7807555	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7812180	0.84[EUR][1000 genomes]
rs9648908	0.84[EUR][1000 genomes]
rs9769767	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv888766	chr7:97975542-98123880	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	esv1795864	chr7:98013507-98040788	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv607919	chr7:98021211-98124854	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
8	nsv539034	chr7:98029119-98106260	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12154723	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs12154723	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98031000-98050400	Weak transcription	Right Atrium	heart
2	chr7:98031400-98046800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:98031800-98047800	Weak transcription	Gastric	stomach
4	chr7:98034200-98038800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:98034400-98038600	Weak transcription	A549	lung
6	chr7:98035200-98040600	Weak transcription	HepG2	liver

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