Variant report

Variant	rs12348304
Chromosome Location	chr9:100611233-100611234
allele	C/T
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	CTBP2	chr9:100610470-100611525	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr9:100610293-100612160	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr9:100609498-100612500	NT2-D1	testis:	n/a	n/a
4	SPI1	chr9:100610865-100611261	HL-60	blood:	n/a	chr9:100611037-100611046 chr9:100611145-100611158 chr9:100611036-100611049 chr9:100611035-100611048
5	POLR2A	chr9:100610987-100611361	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
FOXE1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10046805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10113907	0.81[AFR][1000 genomes]
rs10117642	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10119760	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.82[AFR][1000 genomes]
rs10119853	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10120412	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10122541	0.86[AMR][1000 genomes]
rs10123699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10759975	0.81[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10818124	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818133	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10983958	0.90[ASN][1000 genomes]
rs10983959	0.90[ASN][1000 genomes]
rs10984103	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1156850	0.83[ASN][1000 genomes]
rs12341377	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12343182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12347191	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348691	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287360	0.81[EUR][1000 genomes]
rs13299924	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13300874	0.82[AFR][1000 genomes]
rs13302470	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1443434	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443436	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1867277	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867278	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867280	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1955143	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2120264	0.80[AMR][1000 genomes]
rs2401639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2417576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3021526	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758251	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4297160	0.87[ASN][1000 genomes]
rs4460498	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743139	0.81[EUR][1000 genomes]
rs6478437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478445	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7033315	0.83[AFR][1000 genomes]
rs7033765	0.87[ASN][1000 genomes]
rs7037175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043516	0.82[AFR][1000 genomes]
rs7045138	0.87[ASN][1000 genomes]
rs72753507	0.82[AFR][1000 genomes]
rs72753509	0.82[AFR][1000 genomes]
rs7357707	0.83[AFR][1000 genomes]
rs7851552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851660	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7868534	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7870540	0.83[ASN][1000 genomes]
rs7870795	0.83[ASN][1000 genomes]
rs874004	0.84[AFR][1000 genomes]
rs894673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907581	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs925487	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs993501	0.80[AMR][1000 genomes];0.83[EUR][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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100609800-100611400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:100610000-100611400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr9:100610000-100611800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr9:100610200-100611600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr9:100610400-100611400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr9:100610400-100611400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:100610400-100611400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr9:100610400-100611400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:100610400-100611400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
10	chr9:100610400-100611400	Bivalent Enhancer	Brain Germinal Matrix	brain
11	chr9:100610400-100611400	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
12	chr9:100610400-100611600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr9:100610400-100611600	Bivalent Enhancer	Fetal Brain Male	brain
14	chr9:100610400-100611600	Bivalent Enhancer	Fetal Thymus	thymus
15	chr9:100610400-100611600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
16	chr9:100610400-100612000	Bivalent Enhancer	Spleen	Spleen
17	chr9:100610600-100611400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:100610600-100611400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:100610600-100611400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:100610600-100611400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr9:100610600-100611400	Bivalent Enhancer	Lung	lung
22	chr9:100610600-100611600	Bivalent/Poised TSS	HSMMtube	muscle
23	chr9:100610600-100611800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
24	chr9:100610600-100611800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
25	chr9:100610800-100611400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:100610800-100611400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
27	chr9:100610800-100611400	Flanking Bivalent TSS/Enh	Right Ventricle	heart
28	chr9:100610800-100611400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
29	chr9:100610800-100611400	Bivalent/Poised TSS	NHEK	skin
30	chr9:100610800-100611600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
31	chr9:100610800-100611600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr9:100610800-100611800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
33	chr9:100610800-100611800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
34	chr9:100610800-100611800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr9:100610800-100611800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:100611000-100611400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:100611000-100611400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr9:100611000-100611400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:100611000-100611400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:100611000-100611400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:100611000-100611400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
42	chr9:100611000-100611400	Bivalent Enhancer	Ovary	ovary
43	chr9:100611000-100611400	Flanking Active TSS	Pancreas	Pancrea
44	chr9:100611000-100611400	Flanking Bivalent TSS/Enh	Thymus	Thymus
45	chr9:100611000-100611600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:100611000-100611600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr9:100611000-100611600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
48	chr9:100611000-100611600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
49	chr9:100611000-100611600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
50	chr9:100611000-100611600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--

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