Variant report

Variant	rs10046805
Chromosome Location	chr9:100613956-100613957
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	chr9:100613910-100614092	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:100613782-100614557	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr9:100613920-100614070	WERI-Rb-1	eye:	n/a	n/a
4	CTBP2	chr9:100613864-100616060	H1-hESC	embryonic stem cell:	n/a	n/a
5	SUZ12	chr9:100613856-100618340	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:100613478-100614224	H1-neurons	neurons:	n/a	n/a
7	TCF12	chr9:100613789-100614128	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr9:100613920-100614065	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr9:100613541-100614161	H1-hESC	embryonic stem cell:	n/a	chr9:100613926-100613940
10	MAX	chr9:100613853-100614253	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr9:100613780-100614051	H1-hESC	embryonic stem cell:	n/a	n/a
12	SUZ12	chr9:100612750-100618219	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
FOXE1	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10113884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10113907	0.83[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	0.84[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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818133	0.94[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	0.95[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	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348691	0.95[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	0.84[AFR][1000 genomes]
rs13302470	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1443434	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443435	0.99[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	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867278	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867280	0.98[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	0.95[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	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758248	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758251	0.99[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	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743139	0.81[EUR][1000 genomes]
rs4743140	0.80[AFR][1000 genomes]
rs6478437	0.95[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	0.85[AFR][1000 genomes]
rs7033765	0.87[ASN][1000 genomes]
rs7037175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043516	0.83[AFR][1000 genomes]
rs7045138	0.87[ASN][1000 genomes]
rs72753507	0.84[AFR][1000 genomes]
rs72753509	0.83[AFR][1000 genomes]
rs7357707	0.85[AFR][1000 genomes]
rs7851552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851660	0.90[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	0.85[AFR][1000 genomes]
rs894673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907577	1.00[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:4 , 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
3	nsv825000	chr9:100613121-100618319	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3330300	chr9:100613506-100618154	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100611600-100614000	Weak transcription	Pancreas	Pancrea
2	chr9:100613400-100614000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:100613400-100614000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:100613400-100614000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
5	chr9:100613400-100614000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
6	chr9:100613400-100615400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:100613400-100615600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr9:100613400-100615600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
9	chr9:100613400-100615600	Bivalent Enhancer	Spleen	Spleen
10	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:100613600-100614000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:100613600-100614000	Bivalent/Poised TSS	HMEC	breast
13	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr9:100613600-100615200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
17	chr9:100613600-100618000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr9:100613800-100614000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr9:100613800-100614000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:100613800-100614000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr9:100613800-100614000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
22	chr9:100613800-100614000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:100613800-100614000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:100613800-100614000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
25	chr9:100613800-100614000	Bivalent Enhancer	Brain Germinal Matrix	brain
26	chr9:100613800-100614000	Bivalent Enhancer	Fetal Intestine Small	intestine
27	chr9:100613800-100614000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
28	chr9:100613800-100614000	Bivalent Enhancer	NHDF-Ad	bronchial
29	chr9:100613800-100614000	Bivalent/Poised TSS	NHEK	skin
30	chr9:100613800-100614200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:100613800-100614200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:100613800-100614200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr9:100613800-100614200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr9:100613800-100614200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:100613800-100614200	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
36	chr9:100613800-100614200	Bivalent Enhancer	Gastric	stomach
37	chr9:100613800-100614400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
38	chr9:100613800-100614600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr9:100613800-100614600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:100613800-100614800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:100613800-100615200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr9:100613800-100615400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr9:100613800-100615600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr9:100613800-100615600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
45	chr9:100613800-100615800	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr9:100613800-100616200	Bivalent Enhancer	Liver	Liver
47	chr9:100613800-100616400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:100613800-100616400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr9:100613800-100616400	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr9:100613800-100616400	Bivalent Enhancer	Fetal Stomach	stomach

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