Variant report

Variant	rs58767769
Chromosome Location	chr9:95870628-95870629
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	FOS	chr9:95870524-95870816	MCF10A-Er-Src	breast:	n/a	chr9:95870681-95870693 chr9:95870683-95870691 chr9:95870608-95870620 chr9:95870682-95870692
2	MAZ	chr9:95870399-95870735	K562	blood:	n/a	n/a
3	STAT3	chr9:95870565-95870816	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr9:95870494-95870735	MCF10A-Er-Src	breast:	n/a	n/a
5	BATF	chr9:95870424-95870760	GM12878	blood:	n/a	chr9:95870684-95870694
6	CTCF	chr9:95870538-95872098	SK-N-SH	brain:	n/a	chr9:95871618-95871639 chr9:95871627-95871648 chr9:95871623-95871641 chr9:95871625-95871638 chr9:95871630-95871640 chr9:95871628-95871641 chr9:95871625-95871643 chr9:95871626-95871642 chr9:95871628-95871637
7	EBF1	chr9:95870434-95870734	GM12878	blood:	n/a	n/a
8	JUND	chr9:95870545-95870819	K562	blood:	n/a	chr9:95870681-95870693 chr9:95870683-95870691 chr9:95870608-95870620 chr9:95870682-95870692
9	RCOR1	chr9:95870513-95870836	K562	blood:	n/a	n/a
10	MXI1	chr9:95870524-95872022	SK-N-SH	brain:	n/a	n/a
11	MAFF	chr9:95870527-95870726	K562	blood:	n/a	n/a
12	MAFK	chr9:95870556-95870840	K562	blood:	n/a	chr9:95870681-95870690
13	FOS	chr9:95870549-95870788	MCF10A-Er-Src	breast:	n/a	chr9:95870681-95870693 chr9:95870683-95870691 chr9:95870608-95870620 chr9:95870682-95870692
14	STAT3	chr9:95870518-95870816	MCF10A-Er-Src	breast:	n/a	n/a
15	SMC3	chr9:95870466-95872082	SK-N-SH	brain:	n/a	chr9:95871627-95871641 chr9:95871625-95871639 chr9:95871627-95871634 chr9:95871631-95871641
16	FOS	chr9:95870510-95870822	MCF10A-Er-Src	breast:	n/a	chr9:95870681-95870693 chr9:95870683-95870691 chr9:95870608-95870620 chr9:95870682-95870692

No.	Distal block	Cell Line	Cell type
1	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
2	chr9:95870093..95872225-chr9:96214291..96216786,2	K562	blood:
3	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
4	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:

Variant related genes	Relation type
C9orf89	TF binding region
ENSG00000223446	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10992634	0.95[ASN][1000 genomes]
rs2027585	0.98[AFR][1000 genomes]
rs2275849	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819011	0.95[AFR][1000 genomes]
rs4237219	0.90[AFR][1000 genomes]
rs4333675	0.82[AFR][1000 genomes]
rs4384040	0.85[AFR][1000 genomes]
rs4743885	0.94[AFR][1000 genomes]
rs4744174	0.94[AFR][1000 genomes]
rs55902006	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028778	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7031053	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031737	0.98[ASN][1000 genomes]
rs7868952	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58767769	C9orf89	Cis_1M	lymphoblastoid	RTeQTL
rs58767769	C9orf89	cis	Esophagus Mucosa	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95859400-95876200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
3	chr9:95860200-95872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95860400-95876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:95860800-95872800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:95861600-95872200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:95861800-95882000	Weak transcription	HSMMtube	muscle
8	chr9:95862000-95871200	Weak transcription	Hela-S3	cervix
9	chr9:95862000-95872800	Weak transcription	Osteobl	bone
10	chr9:95862000-95873800	Weak transcription	NH-A	brain
11	chr9:95862000-95878400	Weak transcription	Stomach Mucosa	stomach
12	chr9:95862000-95881800	Weak transcription	HUVEC	blood vessel
13	chr9:95862200-95870800	Weak transcription	Pancreas	Pancrea
14	chr9:95862200-95870800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:95862200-95871600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:95862200-95878000	Weak transcription	HSMM	muscle
17	chr9:95862200-95878600	Weak transcription	Psoas Muscle	Psoas
18	chr9:95862200-95878600	Weak transcription	Right Atrium	heart
19	chr9:95862400-95873000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:95862600-95870800	Weak transcription	Ovary	ovary
21	chr9:95862800-95871200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:95864200-95871600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr9:95866600-95878600	Weak transcription	NHDF-Ad	bronchial
24	chr9:95867000-95878400	Weak transcription	Fetal Lung	lung
25	chr9:95867400-95872200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr9:95867400-95872200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr9:95867600-95871600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr9:95867800-95872800	Weak transcription	Brain Germinal Matrix	brain
29	chr9:95867800-95873400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:95868400-95872600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:95869000-95871000	Enhancers	Fetal Thymus	thymus
32	chr9:95869000-95877600	Strong transcription	Fetal Intestine Small	intestine
33	chr9:95869200-95871200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:95869200-95871400	Strong transcription	Colonic Mucosa	Colon
35	chr9:95869200-95871800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:95869200-95877600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr9:95869400-95870800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:95869400-95871400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:95869400-95877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:95869400-95877400	Strong transcription	NHLF	lung
41	chr9:95869600-95870800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:95869600-95871000	Strong transcription	Fetal Muscle Leg	muscle
43	chr9:95869600-95871000	Strong transcription	Placenta	Placenta
44	chr9:95869600-95871400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:95869600-95871400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:95869600-95871400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr9:95869600-95872200	Enhancers	K562	blood
48	chr9:95869600-95872600	Genic enhancers	Monocytes-CD14+_RO01746	blood
49	chr9:95869600-95876400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:95869600-95877400	Strong transcription	Fetal Stomach	stomach

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