Variant report

Variant	rs73514578
Chromosome Location	chr9:96109050-96109051
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	MAX	chr9:96107900-96109154	H1-hESC	embryonic stem cell:	n/a	chr9:96108823-96108832 chr9:96108823-96108833
3	POLR2A	chr9:96108556-96109113	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr9:96108635-96109071	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr9:96108908-96109069	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:96109016-96109069	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr9:96107960-96109158	H1-hESC	embryonic stem cell:	n/a	chr9:96108823-96108832 chr9:96108823-96108833
8	TBP	chr9:96108398-96109146	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:96108150-96109141	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr9:96107898-96109269	H1-hESC	embryonic stem cell:	n/a	chr9:96108619-96108628 chr9:96108056-96108068 chr9:96108696-96108708
11	CTBP2	chr9:96107924-96109053	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr9:96108675-96109086	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr9:96108269-96109198	H1-hESC	embryonic stem cell:	n/a	chr9:96108619-96108628 chr9:96108696-96108708
14	MXI1	chr9:96108887-96109080	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
C9orf129	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs41308906	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743912	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744194	0.87[ASN][1000 genomes]
rs4744211	0.87[ASN][1000 genomes]
rs4744219	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56948231	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58242432	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616569	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60142142	0.87[ASN][1000 genomes]
rs61584994	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73512403	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73514552	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73514573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

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	chr9:96108000-96109200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr9:96108000-96109200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr9:96108000-96109200	Active TSS	Brain Angular Gyrus	brain
7	chr9:96108000-96109200	Active TSS	Brain Substantia Nigra	brain
8	chr9:96108000-96113000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr9:96108200-96109200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:96108200-96109200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
11	chr9:96108200-96109200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
12	chr9:96108200-96109200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
13	chr9:96108200-96109200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:96108200-96109200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr9:96108200-96109200	Flanking Active TSS	Right Ventricle	heart
16	chr9:96108200-96109200	Bivalent/Poised TSS	NH-A	brain
17	chr9:96108400-96109200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:96108400-96109200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:96108400-96109200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:96108400-96109200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:96108400-96109200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr9:96108400-96109200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:96108400-96109200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:96108400-96109200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr9:96108400-96109200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr9:96108400-96109200	Bivalent Enhancer	Fetal Thymus	thymus
27	chr9:96108400-96109200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
28	chr9:96108400-96109400	Active TSS	Fetal Brain Female	brain
29	chr9:96108400-96109600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr9:96108600-96109200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:96108600-96109200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:96108600-96109200	Active TSS	Rectal Smooth Muscle	rectum
33	chr9:96108600-96109200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr9:96108600-96109200	Bivalent/Poised TSS	NHEK	skin
35	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
36	chr9:96108800-96109200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:96108800-96109200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:96108800-96109200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:96108800-96109200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr9:96108800-96109200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:96108800-96109200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
44	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
45	chr9:96108800-96109200	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr9:96108800-96109200	Enhancers	Fetal Kidney	kidney
48	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr9:96108800-96109200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach

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