Variant report

Variant	rs12347460
Chromosome Location	chr9:96108724-96108725
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	SIN3A	chr9:96107940-96109179	H1-hESC	embryonic stem cell:	n/a	chr9:96108544-96108557
2	CTCF	chr9:96108660-96108810	AG09319	gingival:	n/a	n/a
3	MAX	chr9:96107900-96109154	H1-hESC	embryonic stem cell:	n/a	chr9:96108823-96108832 chr9:96108823-96108833
4	CTCF	chr9:96108720-96108870	SK-N-SH_RA	brain:	n/a	n/a
5	POLR2A	chr9:96108556-96109113	H1-hESC	embryonic stem cell:	n/a	n/a
6	BACH1	chr9:96108635-96109071	H1-hESC	embryonic stem cell:	n/a	n/a
7	GTF2F1	chr9:96108594-96108963	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr9:96108324-96109010	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr9:96108600-96108750	HCM	heart:	n/a	n/a
10	MAX	chr9:96107960-96109158	H1-hESC	embryonic stem cell:	n/a	chr9:96108823-96108832 chr9:96108823-96108833
11	TBP	chr9:96108398-96109146	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr9:96108150-96109141	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr9:96107898-96109269	H1-hESC	embryonic stem cell:	n/a	chr9:96108619-96108628 chr9:96108056-96108068 chr9:96108696-96108708
14	TAF1	chr9:96108591-96108916	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTBP2	chr9:96107924-96109053	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr9:96108168-96108759	H1-hESC	embryonic stem cell:	n/a	chr9:96108660-96108674 chr9:96108628-96108637 chr9:96108622-96108631 chr9:96108475-96108489 chr9:96108482-96108493
17	POLR2A	chr9:96108675-96109086	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr9:96108269-96109198	H1-hESC	embryonic stem cell:	n/a	chr9:96108619-96108628 chr9:96108696-96108708
19	CHD2	chr9:96108248-96108795	H1-hESC	embryonic stem cell:	n/a	chr9:96108730-96108740
20	CTCF	chr9:96108680-96108830	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
C9orf129	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10821107	0.87[ASN][1000 genomes]
rs10821108	0.87[ASN][1000 genomes]
rs10992708	0.81[ASN][1000 genomes]
rs10992709	0.81[ASN][1000 genomes]
rs12685091	0.81[ASN][1000 genomes]
rs2991377	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991384	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2995992	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2995996	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2995997	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2995998	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7042763	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1798245	chr9:96098930-96120432	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv972783	chr9:96104996-96108763	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96107200-96109200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:96107400-96113000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:96107600-96111600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:96107800-96109000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr9:96107800-96109000	Active TSS	Brain Germinal Matrix	brain
6	chr9:96108000-96108800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:96108000-96108800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:96108000-96108800	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr9:96108000-96109000	Active TSS	Brain Anterior Caudate	brain
10	chr9:96108000-96109000	Enhancers	Spleen	Spleen
11	chr9:96108000-96109200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr9:96108000-96109200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:96108000-96109200	Active TSS	Brain Angular Gyrus	brain
14	chr9:96108000-96109200	Active TSS	Brain Substantia Nigra	brain
15	chr9:96108000-96113000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr9:96108200-96108800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr9:96108200-96108800	Bivalent Enhancer	Liver	Liver
18	chr9:96108200-96108800	Active TSS	Fetal Kidney	kidney
19	chr9:96108200-96109000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:96108200-96109000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:96108200-96109000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:96108200-96109200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:96108200-96109200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
24	chr9:96108200-96109200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
25	chr9:96108200-96109200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr9:96108200-96109200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:96108200-96109200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
28	chr9:96108200-96109200	Flanking Active TSS	Right Ventricle	heart
29	chr9:96108200-96109200	Bivalent/Poised TSS	NH-A	brain
30	chr9:96108400-96108800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:96108400-96108800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:96108400-96108800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:96108400-96108800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:96108400-96108800	Bivalent Enhancer	Primary B cells from cord blood	blood
35	chr9:96108400-96108800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr9:96108400-96108800	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr9:96108400-96108800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:96108400-96108800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
39	chr9:96108400-96108800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
40	chr9:96108400-96108800	Bivalent/Poised TSS	Esophagus	oesophagus
41	chr9:96108400-96108800	Bivalent/Poised TSS	Fetal Stomach	stomach
42	chr9:96108400-96108800	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
43	chr9:96108400-96108800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
44	chr9:96108400-96108800	Active TSS	Right Atrium	heart
45	chr9:96108400-96108800	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
46	chr9:96108400-96108800	Bivalent/Poised TSS	Small Intestine	intestine
47	chr9:96108400-96108800	Bivalent/Poised TSS	Thymus	Thymus
48	chr9:96108400-96108800	Bivalent/Poised TSS	NHLF	lung
49	chr9:96108400-96109000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:96108400-96109000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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