Variant report

Variant	rs423477
Chromosome Location	chr9:107981571-107981572
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	chr9:107979211..107982587-chr9:107983640..107987366,3	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10120310	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820792	0.90[CHB][hapmap]
rs10820795	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs10991598	0.90[CHB][hapmap]
rs10991600	0.89[CHB][hapmap]
rs10991601	0.90[CHB][hapmap]
rs10991611	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs10991612	0.90[CHB][hapmap]
rs10991617	0.90[CHB][hapmap]
rs10991618	0.90[CHB][hapmap]
rs12335779	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs12343137	1.00[ASN][1000 genomes]
rs12347364	0.90[CHB][hapmap]
rs12348136	0.90[CHB][hapmap]
rs170582	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs179177	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs182756	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs193007	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs193008	0.81[CHB][hapmap]
rs193009	0.90[CHB][hapmap]
rs2004725	0.90[CHB][hapmap]
rs2100044	0.90[CHB][hapmap]
rs227887	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs227888	0.90[CHB][hapmap]
rs2900397	0.90[CHB][hapmap]
rs327947	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327948	0.90[CHB][hapmap]
rs327950	0.90[CHB][hapmap]
rs327955	0.90[CHB][hapmap]
rs327956	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs327958	0.90[CHB][hapmap]
rs327959	0.90[CHB][hapmap]
rs327960	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327967	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327976	0.90[CHB][hapmap]
rs327982	0.90[CHB][hapmap]
rs327983	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327984	0.90[CHB][hapmap]
rs327985	0.88[CHB][hapmap]
rs327987	0.90[CHB][hapmap]
rs327990	0.90[CHB][hapmap]
rs327991	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327992	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs327993	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327995	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327997	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs327999	0.90[CHB][hapmap]
rs328006	0.90[CHB][hapmap]
rs328007	0.90[CHB][hapmap]
rs328008	0.90[CHB][hapmap]
rs328010	0.90[CHB][hapmap]
rs328012	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs328013	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs328014	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs328015	0.90[CHB][hapmap]
rs328018	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs328019	0.90[CHB][hapmap]
rs328022	0.90[CHB][hapmap]
rs364564	1.00[ASN][1000 genomes]
rs365629	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs366018	1.00[ASN][1000 genomes]
rs372554	1.00[ASN][1000 genomes]
rs372747	1.00[ASN][1000 genomes]
rs375034	0.90[CHB][hapmap]
rs375371	1.00[ASN][1000 genomes]
rs376926	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs378467	0.90[CHB][hapmap]
rs378716	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380104	0.90[CHB][hapmap]
rs383126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs383272	0.90[CHB][hapmap]
rs384924	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs384947	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs386565	0.90[CHB][hapmap]
rs390235	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399707	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401899	1.00[ASN][1000 genomes]
rs405704	1.00[ASN][1000 genomes]
rs409595	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413598	1.00[ASN][1000 genomes]
rs416573	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416641	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs420672	1.00[ASN][1000 genomes]
rs420717	0.90[CHB][hapmap]
rs421342	1.00[ASN][1000 genomes]
rs421495	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422084	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs424495	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs427497	0.98[ASN][1000 genomes]
rs435267	0.98[ASN][1000 genomes]
rs440290	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs442605	0.90[CHB][hapmap]
rs443094	0.90[CHB][hapmap]
rs453041	0.98[ASN][1000 genomes]
rs453378	1.00[ASN][1000 genomes]
rs6479305	0.90[CHB][hapmap]
rs7020982	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs7021008	0.89[CHB][hapmap]
rs7039398	0.90[CHB][hapmap]

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	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv893684	chr9:107893629-108001107	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1043466	chr9:107950174-108001988	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv523889	chr9:107980321-107981571	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs423477	TAL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:107979200-107981800	Weak transcription	Osteobl	bone
2	chr9:107979200-107983200	Weak transcription	Fetal Brain Male	brain
3	chr9:107980000-107989400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:107980600-107983000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:107980800-107982200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr9:107981000-107982200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:107981000-107982200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:107981200-107982000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:107981200-107982200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:107981400-107982200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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