Variant report

Variant	rs9468689
Chromosome Location	chr6:11236899-11236900
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	BHLHE40	chr6:11236571-11236944	GM12878	blood:	n/a	n/a
2	USF1	chr6:11236555-11236922	A549	lung:	n/a	chr6:11236711-11236722
3	RELA	chr6:11236364-11237002	GM19099	blood:	n/a	n/a
4	PBX3	chr6:11236395-11237074	SK-N-SH	brain:	n/a	n/a
5	NFYB	chr6:11236714-11236970	GM12878	blood:	n/a	n/a
6	BHLHE40	chr6:11236569-11236946	HepG2	liver:	n/a	n/a
7	RELA	chr6:11236457-11237006	GM12891	blood:	n/a	n/a
8	PBX3	chr6:11236669-11236930	GM12878	blood:	n/a	n/a
9	RUNX3	chr6:11236558-11236995	GM12878	blood:	n/a	n/a
10	USF1	chr6:11236447-11236961	SK-N-SH	brain:	n/a	chr6:11236711-11236722
11	EBF1	chr6:11236377-11236961	GM12878	blood:	n/a	n/a
12	ZNF143	chr6:11236693-11236994	GM12878	blood:	n/a	n/a
13	GATA3	chr6:11236282-11237024	SK-N-SH	brain:	n/a	chr6:11236362-11236369 chr6:11236474-11236484
14	RELA	chr6:11236596-11236942	GM10847	blood:	n/a	n/a
15	RELA	chr6:11236538-11237006	GM18505	blood:	n/a	n/a
16	PBX3	chr6:11236273-11237064	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr6:11236520-11237057	GM12878	blood:	n/a	n/a
18	RUNX3	chr6:11236572-11237089	GM12878	blood:	n/a	n/a
19	RELA	chr6:11236473-11236974	GM18951	blood:	n/a	n/a
20	EP300	chr6:11236626-11236913	GM12878	blood:	n/a	n/a
21	USF2	chr6:11236532-11236943	GM12878	blood:	n/a	n/a
22	TCF12	chr6:11236158-11237079	SK-N-SH	brain:	n/a	chr6:11236192-11236202
23	RELA	chr6:11236489-11236966	GM19193	blood:	n/a	n/a
24	CTCF	chr6:11236860-11237010	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11235150..11238104-chr6:11239000..11242242,3	K562	blood:
2	chr6:11228247..11230066-chr6:11234822..11237148,2	MCF-7	breast:
3	chr6:11234125..11238203-chr6:11239752..11242885,4	MCF-7	breast:
4	chr6:11235150..11238104-chr6:11238478..11241359,3	K562	blood:
5	chr6:11233234..11235237-chr6:11235574..11238401,2	K562	blood:

Variant related genes	Relation type
NEDD9	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3734406	1.00[AMR][1000 genomes]
rs56128589	1.00[AMR][1000 genomes]
rs58174898	1.00[AMR][1000 genomes]
rs73721655	1.00[AMR][1000 genomes]
rs73721660	1.00[AMR][1000 genomes]
rs73721685	1.00[AMR][1000 genomes]
rs73723906	1.00[AMR][1000 genomes]
rs73723908	1.00[AMR][1000 genomes]
rs73723919	1.00[AMR][1000 genomes]
rs9468538	1.00[AMR][1000 genomes]
rs9468564	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11233400-11237200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:11233600-11241800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:11233800-11238400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:11233800-11238600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:11233800-11241600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:11234000-11241800	Weak transcription	NHLF	lung
7	chr6:11234000-11242200	Weak transcription	Brain Anterior Caudate	brain
8	chr6:11234000-11242200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:11234200-11241800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:11234400-11237200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:11234400-11238600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:11234400-11241600	Weak transcription	Aorta	Aorta
13	chr6:11234400-11241800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:11234400-11241800	Weak transcription	Right Ventricle	heart
15	chr6:11234400-11249600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:11234600-11237800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:11234600-11248400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:11234800-11238000	Enhancers	HepG2	liver
19	chr6:11234800-11241600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:11234800-11242200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:11234800-11251400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:11235000-11257200	Weak transcription	Dnd41	blood
23	chr6:11235600-11237000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:11235600-11237400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:11235600-11237600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:11235600-11237600	Enhancers	NHEK	skin
27	chr6:11235800-11237000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:11235800-11237000	Enhancers	A549	lung
29	chr6:11235800-11237400	Enhancers	Placenta	Placenta
30	chr6:11235800-11237600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:11235800-11237600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:11235800-11237800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:11235800-11237800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:11235800-11237800	Enhancers	Fetal Brain Female	brain
35	chr6:11235800-11238800	Enhancers	Fetal Brain Male	brain
36	chr6:11236000-11237000	Enhancers	Fetal Heart	heart
37	chr6:11236000-11237200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:11236000-11237200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:11236000-11237200	Enhancers	Duodenum Mucosa	Duodenum
40	chr6:11236000-11237200	Enhancers	Fetal Kidney	kidney
41	chr6:11236000-11237400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:11236000-11237400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:11236000-11237400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:11236000-11237600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:11236000-11237600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:11236000-11237600	Enhancers	Lung	lung
47	chr6:11236200-11237200	Enhancers	Adipose Nuclei	Adipose
48	chr6:11236200-11237400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:11236200-11237400	Enhancers	Fetal Intestine Large	intestine
50	chr6:11236200-11237600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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