Variant report

Variant	rs12539997
Chromosome Location	chr7:87131423-87131424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1014283	0.89[EUR][1000 genomes]
rs10452935	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10452936	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1055302	0.87[ASN][1000 genomes]
rs11974333	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11975741	0.86[EUR][1000 genomes]
rs12538707	0.97[ASN][1000 genomes]
rs12539936	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12672720	0.97[ASN][1000 genomes]
rs12673662	0.93[ASN][1000 genomes]
rs1468615	0.89[EUR][1000 genomes]
rs1473152	0.89[EUR][1000 genomes]
rs1473154	0.89[EUR][1000 genomes]
rs1558375	0.89[EUR][1000 genomes]
rs1558376	0.89[EUR][1000 genomes]
rs17149644	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17209662	0.97[ASN][1000 genomes]
rs17209837	0.97[ASN][1000 genomes]
rs17275514	0.97[ASN][1000 genomes]
rs2071645	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072384	0.87[EUR][1000 genomes]
rs2109505	0.89[EUR][1000 genomes]
rs2270187	0.89[EUR][1000 genomes]
rs2888611	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3842	0.83[ASN][1000 genomes]
rs4148805	0.93[ASN][1000 genomes]
rs4148807	0.92[ASN][1000 genomes]
rs4148808	0.93[ASN][1000 genomes]
rs4148810	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4148811	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4148813	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4148816	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4148818	0.89[EUR][1000 genomes]
rs4148820	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4148821	0.87[EUR][1000 genomes]
rs4148824	0.88[EUR][1000 genomes]
rs4148826	0.89[EUR][1000 genomes]
rs45478299	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45479991	0.89[EUR][1000 genomes]
rs45493392	0.87[EUR][1000 genomes]
rs45496691	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45537841	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45553044	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs45560338	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55747905	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60040620	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60541816	0.97[ASN][1000 genomes]
rs60624924	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60916103	0.97[ASN][1000 genomes]
rs66510518	0.95[ASN][1000 genomes]
rs6971521	0.89[EUR][1000 genomes]
rs6971745	0.86[EUR][1000 genomes]
rs73198345	0.97[ASN][1000 genomes]
rs7782186	0.83[EUR][1000 genomes]
rs7789645	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793196	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802555	0.97[ASN][1000 genomes]
rs7802783	0.97[ASN][1000 genomes]
rs998671	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv1828294	chr7:86857553-87147397	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv3382480	chr7:87031452-87133648	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv464623	chr7:87040629-87139316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv607726	chr7:87040629-87139316	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	esv3447637	chr7:87130891-87133089	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3436896	chr7:87131416-87132664	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12539997	ABCB4	Cis_1M	lymphoblastoid	RTeQTL
rs12539997	ABCB1///ABCB4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87126600-87138200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:87128000-87133600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:87128000-87134400	Weak transcription	Primary T cells from cord blood	blood
4	chr7:87128200-87132600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:87128200-87134200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:87128200-87134600	Weak transcription	HepG2	liver
7	chr7:87128200-87134800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr7:87128600-87132800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:87129200-87134200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:87129200-87136200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:87129400-87138200	Weak transcription	Primary B cells from cord blood	blood
12	chr7:87129800-87134800	Weak transcription	Liver	Liver
13	chr7:87130000-87135200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr7:87130600-87133600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:87131000-87134800	Weak transcription	Placenta	Placenta

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