Variant report

Variant	rs999690
Chromosome Location	chr21:47647077-47647078
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	POLR2A	chr21:47646915-47647414	Raji	blood:	n/a	n/a
2	FOS	chr21:47646705-47647204	MCF10A-Er-Src	breast:	n/a	chr21:47647037-47647045 chr21:47646791-47646800
3	WRNIP1	chr21:47647040-47647335	GM12878	blood:	n/a	n/a
4	POU2F2	chr21:47646772-47647220	GM12891	blood:	n/a	n/a
5	RELA	chr21:47646392-47647232	GM19099	blood:	n/a	chr21:47646917-47646926 chr21:47646917-47646926
6	POLR2A	chr21:47646766-47647504	GM12878	blood:	n/a	n/a
7	MTA3	chr21:47646683-47647341	GM12878	blood:	n/a	n/a
8	TBP	chr21:47646575-47647405	GM12878	blood:	n/a	n/a
9	POLR2A	chr21:47646925-47647194	GM12878	blood:	n/a	n/a
10	POLR2A	chr21:47646651-47647226	MCF10A-Er-Src	breast:	n/a	n/a
11	ZNF143	chr21:47646793-47647293	GM12878	blood:	n/a	chr21:47646962-47646977
12	MXI1	chr21:47646525-47647212	GM12878	blood:	n/a	n/a
13	ZNF263	chr21:47646983-47647560	HEK293-T-REx	kidney:	n/a	chr21:47647193-47647214 chr21:47647204-47647213
14	POLR2A	chr21:47646437-47647552	MCF10A-Er-Src	breast:	n/a	n/a
15	RCOR1	chr21:47646961-47647157	K562	blood:	n/a	n/a
16	RCOR1	chr21:47646803-47647162	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr21:47646897-47647283	GM12878	blood:	n/a	n/a
18	STAT1	chr21:47646915-47647120	GM12878	blood:	n/a	n/a
19	BHLHE40	chr21:47646103-47647257	GM12878	blood:	n/a	n/a
20	POLR2A	chr21:47646979-47647226	HepG2	liver:	n/a	n/a
21	CHD2	chr21:47646800-47647243	GM12878	blood:	n/a	n/a
22	POLR2A	chr21:47646117-47647479	GM12891	blood:	n/a	n/a
23	TBL1XR1	chr21:47646899-47647178	K562	blood:	n/a	n/a
24	CUX1	chr21:47646730-47647080	GM12878	blood:	n/a	n/a
25	EBF1	chr21:47646060-47647312	GM12878	blood:	n/a	n/a
26	POLR2A	chr21:47646817-47647786	GM12878	blood:	n/a	n/a
27	MXI1	chr21:47646983-47649758	IMR90	lung:	n/a	n/a
28	GATA1	chr21:47646992-47648126	PBDE	blood:	n/a	n/a
29	POLR2A	chr21:47646963-47647278	GM12878	blood:	n/a	n/a
30	POLR2A	chr21:47646866-47647334	GM12878	blood:	n/a	n/a
31	RCOR1	chr21:47647061-47647200	HepG2	liver:	n/a	n/a
32	POLR2A	chr21:47646896-47647546	IMR90	lung:	n/a	n/a
33	POLR2A	chr21:47646778-47647396	GM12878	blood:	n/a	n/a
34	RELA	chr21:47646773-47647182	GM10847	blood:	n/a	chr21:47646917-47646926 chr21:47646917-47646926

No.	Distal block	Cell Line	Cell type
1	chr21:47646324..47649299-chr21:47673752..47676483,2	K562	blood:
2	chr21:47633762..47640190-chr21:47646866..47650293,7	MCF-7	breast:
3	chr21:47645527..47650637-chr21:47703398..47707562,6	MCF-7	breast:
4	chr21:47639961..47644801-chr21:47645631..47650469,7	K562	blood:
5	chr21:47646929..47655402-chr21:47657205..47667464,13	MCF-7	breast:
6	chr21:47646269..47649125-chr21:47743785..47746480,4	MCF-7	breast:
7	chr21:47645020..47650682-chr21:47742361..47746485,6	MCF-7	breast:
8	chr21:47562180..47565264-chr21:47646835..47649294,3	MCF-7	breast:
9	chr21:47639839..47642625-chr21:47644945..47648967,4	K562	blood:
10	chr21:47646904..47649112-chr21:47706461..47708002,3	MCF-7	breast:
11	chr21:47646455..47648066-chr21:47714633..47716764,2	MCF-7	breast:
12	chr21:47601827..47605045-chr21:47646095..47649627,4	MCF-7	breast:

Variant related genes	Relation type
MCM3AP-AS1	TF binding region
ENSG00000223901	Chromatin interaction
ENSG00000160298	Chromatin interaction
ENSG00000182362	Chromatin interaction
ENSG00000160282	Chromatin interaction
ENSG00000228404	Chromatin interaction
ENSG00000228137	Chromatin interaction
ENSG00000160284	Chromatin interaction
ENSG00000239415	Chromatin interaction
ENSG00000160294	Chromatin interaction
ENSG00000160299	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13052767	0.96[AFR][1000 genomes]
rs16978977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17176653	0.87[AFR][1000 genomes]
rs17177037	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2839148	0.89[AFR][1000 genomes]
rs28459212	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6518279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7281075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7283013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7283945	0.81[AFR][1000 genomes]
rs8130539	0.89[AFR][1000 genomes]
rs999689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
4	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
5	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
6	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
7	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
8	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
9	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
10	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
12	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
13	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
14	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
15	nsv914101	chr21:47491014-47650362	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
16	nsv914116	chr21:47535248-47650362	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
17	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
18	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
19	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
20	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
21	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
22	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
23	nsv914134	chr21:47632995-47712185	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	n/a
24	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47642600-47647200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr21:47643200-47647200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:47645200-47647200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr21:47645200-47647200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr21:47645200-47647200	Enhancers	Ovary	ovary
6	chr21:47645200-47647600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr21:47645600-47648400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr21:47645800-47647400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
9	chr21:47645800-47647600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:47645800-47647800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr21:47645800-47647800	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr21:47646000-47647400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr21:47646000-47647400	Enhancers	Stomach Mucosa	stomach
14	chr21:47646000-47647600	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr21:47646000-47647600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr21:47646000-47648000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr21:47646200-47647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr21:47646200-47647200	Enhancers	Fetal Thymus	thymus
19	chr21:47646200-47647200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
20	chr21:47646200-47647400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr21:47646200-47647400	Enhancers	Primary T cells from cord blood	blood
22	chr21:47646200-47647400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:47646200-47647400	Enhancers	Colon Smooth Muscle	Colon
24	chr21:47646200-47647400	Transcr. at gene 5' and 3'	K562	blood
25	chr21:47646200-47647600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:47646200-47647600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr21:47646200-47647600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr21:47646200-47647600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr21:47646200-47647600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr21:47646200-47647600	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr21:47646200-47647600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr21:47646200-47647800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr21:47646200-47647800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr21:47646200-47647800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr21:47646200-47647800	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr21:47646200-47647800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr21:47646200-47647800	Enhancers	Fetal Lung	lung
38	chr21:47646200-47647800	Enhancers	Spleen	Spleen
39	chr21:47646200-47648000	Flanking Active TSS	Fetal Brain Female	brain
40	chr21:47646200-47648000	Flanking Active TSS	HUVEC	blood vessel
41	chr21:47646200-47648200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr21:47646200-47649800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr21:47646400-47647200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr21:47646400-47647600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr21:47646400-47647600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr21:47646400-47647800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr21:47646600-47647200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr21:47646600-47647200	Weak transcription	Aorta	Aorta
49	chr21:47646600-47647400	Flanking Active TSS	HepG2	liver
50	chr21:47646600-47647600	Enhancers	Primary hematopoietic stem cells	blood

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