Variant report

Variant	rs11789875
Chromosome Location	chr9:16872323-16872324
allele	A/G
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	PBX3	chr9:16871583-16872340	SK-N-SH	brain:	n/a	n/a
2	MAZ	chr9:16869593-16872539	IMR90	lung:	n/a	chr9:16871181-16871190 chr9:16871535-16871545
3	MEF2A	chr9:16871787-16872323	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr9:16871507-16872470	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr9:16870465-16872409	SK-N-SH	brain:	n/a	n/a
6	EP300	chr9:16870388-16872376	SK-N-SH	brain:	n/a	chr9:16870934-16870948
7	TCF12	chr9:16871551-16872333	SK-N-SH	brain:	n/a	n/a
8	SIN3A	chr9:16869268-16872426	H1-hESC	embryonic stem cell:	n/a	chr9:16870165-16870178
9	GATA3	chr9:16871487-16872438	SK-N-SH	brain:	n/a	chr9:16872178-16872189
10	FOS	chr9:16871719-16872332	HUVEC	blood vessel:	n/a	n/a
11	PBX3	chr9:16871561-16872377	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr9:16871716-16872364	SK-N-SH	brain:	n/a	chr9:16872331-16872340

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]
rs10962649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16867600-16872400	Active TSS	Ovary	ovary
2	chr9:16868400-16872400	Active TSS	Rectal Smooth Muscle	rectum
3	chr9:16868800-16872400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr9:16869000-16872400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:16869400-16872400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr9:16869400-16872400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:16869600-16872400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr9:16869600-16872400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:16869600-16872400	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr9:16869800-16872400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:16869800-16872400	Bivalent/Poised TSS	Thymus	Thymus
12	chr9:16870000-16872400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
13	chr9:16870200-16872400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:16870200-16872400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr9:16871200-16872400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:16871400-16872400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:16871600-16872400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:16871600-16872400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr9:16871800-16872400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:16871800-16872400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:16871800-16872400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr9:16871800-16872400	Enhancers	Liver	Liver
23	chr9:16871800-16872400	Flanking Active TSS	HUVEC	blood vessel
24	chr9:16872000-16872400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:16872000-16872400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr9:16872000-16872400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr9:16872000-16872400	Active TSS	Brain Hippocampus Middle	brain
28	chr9:16872000-16872400	Active TSS	Fetal Muscle Trunk	muscle
29	chr9:16872000-16872400	Flanking Active TSS	Fetal Stomach	stomach
30	chr9:16872000-16872400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr9:16872000-16872400	Flanking Active TSS	A549	lung
32	chr9:16872000-16872400	Flanking Active TSS	HSMMtube	muscle
33	chr9:16872000-16872400	Flanking Active TSS	NH-A	brain
34	chr9:16872000-16872400	Flanking Active TSS	NHDF-Ad	bronchial
35	chr9:16872000-16872400	Flanking Active TSS	NHEK	skin
36	chr9:16872000-16872400	Flanking Active TSS	Osteobl	bone
37	chr9:16872000-16872600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr9:16872000-16885000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:16872200-16872400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:16872200-16872400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr9:16872200-16872400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr9:16872200-16872400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:16872200-16872400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:16872200-16872400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:16872200-16872400	Bivalent Enhancer	Primary T cells from cord blood	blood
46	chr9:16872200-16872400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:16872200-16872400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
48	chr9:16872200-16872400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:16872200-16872400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:16872200-16872400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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