Variant report

Variant	rs28728356
Chromosome Location	chr21:46221494-46221495
allele	C/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	chr21:46221452-46222061	K562	blood:	n/a	n/a
2	POLR2A	chr21:46221272-46222146	H1-neurons	neurons:	n/a	n/a
3	GABPA	chr21:46221037-46222269	HL-60	blood:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
4	MAX	chr21:46220947-46222556	Hela-S3	cervix:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
5	SREBP2	chr21:46220984-46222111	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:46221379-46222482	PANC-1	pancreas:	n/a	n/a
7	ZMIZ1	chr21:46221261-46222005	K562	blood:	n/a	n/a
8	MYC	chr21:46221051-46222484	A549	lung:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
9	POLR2A	chr21:46220923-46223514	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr21:46221343-46222618	H1-hESC	embryonic stem cell:	n/a	n/a
11	HEY1	chr21:46221478-46222047	HepG2	liver:	n/a	chr21:46221518-46221533
12	GABPA	chr21:46221407-46222146	A549	lung:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
13	POLR2A	chr21:46221416-46222547	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr21:46221484-46222573	HCT-116	colon:	n/a	n/a
15	GABPA	chr21:46220816-46222492	MCF-7	breast:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
16	JUND	chr21:46220780-46221986	K562	blood:	n/a	n/a
17	FOXP2	chr21:46221368-46222070	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr21:46221444-46222951	GM18951	blood:	n/a	n/a
19	POLR2A	chr21:46221357-46223210	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr21:46220971-46222659	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
21	POLR2A	chr21:46221487-46222353	HepG2	liver:	n/a	n/a
22	POLR2A	chr21:46220877-46225649	K562	blood:	n/a	n/a
23	ETS1	chr21:46221404-46221899	K562	blood:	n/a	n/a
24	POLR2A	chr21:46221284-46222094	HUVEC	blood vessel:	n/a	n/a
25	RUNX3	chr21:46221479-46222079	GM12878	blood:	n/a	n/a
26	SIN3A	chr21:46220887-46222973	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr21:46221404-46222699	Hela-S3	cervix:	n/a	n/a
28	HEY1	chr21:46221439-46222096	K562	blood:	n/a	chr21:46221518-46221533
29	ELF1	chr21:46221346-46222481	GM12878	blood:	n/a	chr21:46221512-46221524 chr21:46222336-46222348
30	POLR2A	chr21:46220980-46225308	K562	blood:	n/a	n/a
31	POLR2A	chr21:46221338-46225872	GM12878	blood:	n/a	n/a
32	CTCF	chr21:46220909-46221498	GM12878	blood:	n/a	n/a
33	TBP	chr21:46220886-46222735	K562	blood:	n/a	n/a
34	MAX	chr21:46221015-46223263	HepG2	liver:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
35	POLR2A	chr21:46221413-46223236	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr21:46221360-46221510	NHEK	skin:	n/a	n/a
37	POLR2A	chr21:46221462-46222080	K562	blood:	n/a	n/a
38	CCNT2	chr21:46221412-46222553	K562	blood:	n/a	chr21:46221544-46221553 chr21:46222087-46222096
39	GABPA	chr21:46221472-46222037	Hela-S3	cervix:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
40	BCLAF1	chr21:46221447-46222088	GM12878	blood:	n/a	chr21:46221519-46221532 chr21:46221454-46221467
41	ZBTB7A	chr21:46221368-46221874	K562	blood:	n/a	n/a
42	POLR2A	chr21:46220710-46226000	K562	blood:	n/a	n/a
43	GATA1	chr21:46220892-46221894	PBDE	blood:	n/a	n/a
44	MAX	chr21:46220910-46222976	MCF-7	breast:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
45	POLR2A	chr21:46220981-46225932	K562	blood:	n/a	n/a
46	POLR2A	chr21:46221318-46222536	MCF-7	breast:	n/a	n/a
47	GABPA	chr21:46221461-46222047	H1-hESC	embryonic stem cell:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
48	POLR2A	chr21:46221425-46222042	SK-N-MC	brain:	n/a	n/a
49	MAX	chr21:46221032-46222559	A549	lung:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
50	MYC	chr21:46220905-46223032	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243

No.	Distal block	Cell Line	Cell type
1	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
2	chr21:46220374..46222087-chr21:46311415..46314337,2	MCF-7	breast:
3	chr21:45928985..45931297-chr21:46219796..46221889,2	MCF-7	breast:
4	chr15:65809487..65810260-chr21:46221235..46221786,2	NB4	blood:
5	chr21:46218558..46223428-chr21:46289542..46296056,15	MCF-7	breast:
6	chr21:45718752..45721154-chr21:46219831..46222611,2	K562	blood:
7	chr21:46220974..46223841-chr21:46346856..46349461,2	K562	blood:
8	chr21:46220554..46223722-chr21:46306934..46310028,3	MCF-7	breast:
9	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
10	chr21:46220726..46223224-chr21:46328113..46331561,4	K562	blood:
11	chr21:46219434..46222664-chr21:46346417..46349763,6	MCF-7	breast:
12	chr21:46220151..46222677-chr21:46492186..46495962,3	K562	blood:
13	chr12:58145700..58146231-chr21:46221321..46221873,2	Hela-S3	cervix:
14	chr12:27676440..27677164-chr21:46221167..46221923,2	Hela-S3	cervix:
15	chr21:46220930..46225769-chr21:46292170..46294469,5	K562	blood:
16	chr21:46218496..46222154-chr21:46279503..46283710,3	MCF-7	breast:
17	chr21:46221113..46222920-chr21:46311601..46314491,2	K562	blood:
18	chr1:78148402..78149137-chr21:46221447..46222054,2	Hela-S3	cervix:
19	chr21:46220413..46223818-chr21:46291771..46295209,8	K562	blood:
20	chr21:46220308..46222402-chr21:46328701..46333083,4	MCF-7	breast:
21	chr21:45927714..45931885-chr21:46220128..46224260,6	MCF-7	breast:
22	chr21:46220260..46222802-chr21:46358731..46365262,8	MCF-7	breast:
23	chr20:45984634..45987262-chr21:46219843..46222143,2	MCF-7	breast:
24	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
25	chr21:46220263..46223201-chr21:46349640..46352735,4	K562	blood:
26	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

Variant related genes	Relation type
ENSG00000236519	TF binding region
ENSG00000273027	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000235890	Chromatin interaction
ENSG00000110841	Chromatin interaction
ENSG00000074603	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000036549	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000183255	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1051331	0.85[EUR][1000 genomes]
rs1141	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17217834	0.96[EUR][1000 genomes]
rs17289578	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17289745	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2017089	0.95[EUR][1000 genomes]
rs2838689	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2838690	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2838691	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2838692	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs428428	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73232950	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8645	0.85[EUR][1000 genomes]
rs873301	0.96[EUR][1000 genomes]
rs9977480	0.85[EUR][1000 genomes]
rs9977684	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9984357	0.84[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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46219800-46222400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr21:46220000-46221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr21:46220000-46222400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr21:46220200-46221600	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr21:46220200-46222600	Active TSS	Fetal Kidney	kidney
6	chr21:46220200-46222600	Active TSS	A549	lung
7	chr21:46220400-46221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:46220400-46221600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr21:46220400-46221600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr21:46220400-46221600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr21:46220400-46222000	Active TSS	Fetal Muscle Trunk	muscle
12	chr21:46220400-46222600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr21:46220400-46222800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:46220400-46223000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr21:46220600-46222200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr21:46220600-46222400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:46220600-46222400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:46220600-46222400	Active TSS	Fetal Intestine Large	intestine
19	chr21:46220600-46222600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr21:46220600-46222600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr21:46220600-46222800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:46220600-46222800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr21:46220600-46222800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr21:46220800-46222200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:46220800-46222200	Active TSS	Pancreas	Pancrea
26	chr21:46220800-46222400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr21:46220800-46222400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr21:46220800-46222400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:46220800-46222400	Active TSS	Aorta	Aorta
30	chr21:46220800-46222400	Bivalent/Poised TSS	HepG2	liver
31	chr21:46220800-46222400	Active TSS	HSMMtube	muscle
32	chr21:46220800-46222600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr21:46220800-46222600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:46220800-46222600	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr21:46220800-46222600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr21:46220800-46222600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr21:46220800-46222600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr21:46220800-46222600	Active TSS	NHLF	lung
39	chr21:46220800-46222800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr21:46220800-46222800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr21:46220800-46222800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr21:46220800-46222800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr21:46220800-46223000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr21:46220800-46223000	Active TSS	HSMM	muscle
45	chr21:46221000-46221600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr21:46221000-46221600	Transcr. at gene 5' and 3'	Placenta Amnion	Placenta Amnion
47	chr21:46221000-46221800	Active TSS	Colonic Mucosa	Colon
48	chr21:46221000-46222000	Active TSS	Fetal Brain Male	brain
49	chr21:46221000-46222200	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr21:46221000-46222200	Active TSS	Brain Inferior Temporal Lobe	brain

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