Variant report

Variant	rs16845066
Chromosome Location	chr1:172872956-172872957
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	GATA3	chr1:172871732-172873627	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr1:172872627-172873300	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr1:172872680-172873029	HUVEC	blood vessel:	n/a	n/a
4	FOS	chr1:172872703-172873048	Hela-S3	cervix:	n/a	n/a
5	TCF12	chr1:172872511-172873268	SK-N-SH	brain:	n/a	n/a
6	FOSL1	chr1:172872597-172873198	HCT-116	colon:	n/a	chr1:172873060-172873072
7	POLR2A	chr1:172872717-172873049	HCT-116	colon:	n/a	n/a
8	SP1	chr1:172872411-172873640	HCT-116	colon:	n/a	n/a
9	EP300	chr1:172872715-172873052	Hela-S3	cervix:	n/a	chr1:172872778-172872786
10	RXRA	chr1:172872536-172873138	SK-N-SH	brain:	n/a	n/a
11	JUN	chr1:172872691-172873025	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:172872626-172873157	HUVEC	blood vessel:	n/a	n/a
13	TCF7L2	chr1:172872729-172872998	Hela-S3	cervix:	n/a	n/a
14	SP1	chr1:172872563-172873211	HCT-116	colon:	n/a	n/a
15	POLR2A	chr1:172872670-172873135	SK-N-SH	brain:	n/a	n/a
16	FOSL1	chr1:172872579-172873095	HCT-116	colon:	n/a	chr1:172873060-172873072
17	JUND	chr1:172872636-172873136	SK-N-SH	brain:	n/a	chr1:172873060-172873072
18	GATA3	chr1:172872560-172873380	SK-N-SH	brain:	n/a	n/a
19	JUND	chr1:172872563-172873192	HCT-116	colon:	n/a	chr1:172873060-172873072
20	POLR2A	chr1:172872603-172873757	HUVEC	blood vessel:	n/a	n/a
21	FOS	chr1:172871925-172872981	MCF10A-Er-Src	breast:	n/a	chr1:172872067-172872078 chr1:172872109-172872119
22	FOS	chr1:172872686-172873016	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr1:172872692-172873082	HUVEC	blood vessel:	n/a	chr1:172873060-172873072
24	FOSL2	chr1:172872574-172873106	SK-N-SH	brain:	n/a	chr1:172873060-172873072
25	CEBPB	chr1:172871962-172873124	Hela-S3	cervix:	n/a	n/a
26	JUND	chr1:172872572-172873252	HCT-116	colon:	n/a	chr1:172873060-172873072
27	TCF12	chr1:172871806-172873267	SK-N-SH	brain:	n/a	n/a
28	EP300	chr1:172872560-172873312	SK-N-SH	brain:	n/a	chr1:172872778-172872786

Variant related genes	Relation type
ENSG00000224000	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10912521	1.00[EUR][1000 genomes]
rs13375250	1.00[EUR][1000 genomes]
rs13375545	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16845043	1.00[EUR][1000 genomes]
rs2206374	1.00[EUR][1000 genomes]
rs35344763	1.00[EUR][1000 genomes]
rs56962913	1.00[EUR][1000 genomes]
rs58852323	1.00[EUR][1000 genomes]
rs60924937	1.00[EUR][1000 genomes]
rs6662600	1.00[EUR][1000 genomes]
rs74128727	1.00[EUR][1000 genomes]
rs74128728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74128729	1.00[EUR][1000 genomes]
rs74128735	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7521017	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3587	chr1:172836950-172882218	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172865200-172875200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:172865600-172874600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:172865800-172875200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:172865800-172878400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:172869600-172876800	Enhancers	NHLF	lung
6	chr1:172870000-172874800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:172870000-172874800	Weak transcription	Dnd41	blood
8	chr1:172870000-172875000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:172870000-172875200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:172870200-172874000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:172870200-172875200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:172870400-172874800	Weak transcription	Primary T cells from cord blood	blood
13	chr1:172870400-172875000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:172870400-172875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:172870800-172874600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:172870800-172874800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:172870800-172875200	Weak transcription	Primary B cells from cord blood	blood
18	chr1:172870800-172875400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:172870800-172875800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:172871000-172876600	Enhancers	HSMM	muscle
21	chr1:172871200-172876200	Enhancers	HUVEC	blood vessel
22	chr1:172871200-172877000	Enhancers	NHDF-Ad	bronchial
23	chr1:172871200-172877200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:172871400-172873000	Enhancers	NH-A	brain
25	chr1:172871400-172873600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:172871400-172874400	Enhancers	Hela-S3	cervix
27	chr1:172871400-172875200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:172871400-172876400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:172871400-172876800	Enhancers	Osteobl	bone
30	chr1:172871400-172877000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:172871600-172873400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:172871600-172874200	Enhancers	NHEK	skin
33	chr1:172871600-172875200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:172871600-172877000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:172872000-172873800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:172872000-172873800	Enhancers	A549	lung
37	chr1:172872200-172876400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:172872200-172876600	Enhancers	HSMMtube	muscle
39	chr1:172872200-172876800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:172872200-172876800	Enhancers	HMEC	breast
41	chr1:172872400-172876600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:172872600-172877000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:172872800-172876800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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