Variant report

Variant	rs10962649
Chromosome Location	chr9:16873535-16873536
allele	C/T
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	CEBPB	chr9:16873182-16873748	IMR90	lung:	n/a	chr9:16873434-16873445
2	CEBPB	chr9:16873187-16873697	Hela-S3	cervix:	n/a	chr9:16873434-16873445

Variant related genes	Relation type
BNC2	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10962638	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10962642	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10962645	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962647	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962648	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10962653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10962656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10962658	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10962659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11788047	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11789875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11792249	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12379687	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62541877	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62541878	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62541879	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62541920	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62541922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62541923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62541926	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62543561	0.83[AFR][1000 genomes]
rs62543578	0.83[AFR][1000 genomes]
rs62543579	0.83[AFR][1000 genomes]
rs62543581	0.83[AFR][1000 genomes]
rs62543582	0.83[AFR][1000 genomes]
rs62543583	0.83[AFR][1000 genomes]
rs62543584	0.83[AFR][1000 genomes]
rs62543585	0.83[AFR][1000 genomes]
rs72713890	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv1018615	chr9:16865804-16960970	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	nsv540074	chr9:16865804-16960970	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16872000-16885000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16872200-16874400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:16872200-16879400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:16872400-16873600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:16872400-16873600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:16872400-16873800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:16872400-16873800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:16872400-16873800	Enhancers	NHLF	lung
9	chr9:16872400-16874000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:16872400-16874000	Enhancers	NHDF-Ad	bronchial
11	chr9:16872600-16873600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:16873000-16874000	Enhancers	A549	lung
13	chr9:16873000-16874200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr9:16873200-16873800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr9:16873200-16873800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:16873200-16873800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:16873200-16874000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:16873400-16873600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:16873400-16873600	Enhancers	Fetal Stomach	stomach
20	chr9:16873400-16873600	Enhancers	Osteobl	bone
21	chr9:16873400-16873800	Enhancers	NH-A	brain
22	chr9:16873400-16874000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr9:16873400-16874000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr9:16873400-16874000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr9:16873400-16874000	Enhancers	Rectal Smooth Muscle	rectum
26	chr9:16873400-16874200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr9:16873400-16874600	Enhancers	H9 Cell Line	embryonic stem cell

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