Variant report

Variant	rs539461785
Chromosome Location	chr21:46224941-46224942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46224679-46225405	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr21:46224628-46225037	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:46224273-46225112	K562	blood:	n/a	n/a
4	POLR2A	chr21:46224871-46226057	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr21:46223597-46225876	HEK293	kidney:	n/a	n/a
6	POLR2A	chr21:46220877-46225649	K562	blood:	n/a	n/a
7	POLR2A	chr21:46224629-46225208	GM12892	blood:	n/a	n/a
8	POLR2A	chr21:46220980-46225308	K562	blood:	n/a	n/a
9	POLR2A	chr21:46221338-46225872	GM12878	blood:	n/a	n/a
10	POLR2A	chr21:46223465-46225324	HCT-116	colon:	n/a	n/a
11	POLR2A	chr21:46220710-46226000	K562	blood:	n/a	n/a
12	POLR2A	chr21:46224691-46225020	GM12878	blood:	n/a	n/a
13	POLR2A	chr21:46220981-46225932	K562	blood:	n/a	n/a
14	POLR2A	chr21:46224710-46225366	K562	blood:	n/a	n/a
15	POLR2A	chr21:46224743-46224948	GM12878	blood:	n/a	n/a
16	POLR2A	chr21:46220458-46225731	K562	blood:	n/a	n/a
17	REST	chr21:46224713-46225002	SK-N-SH	brain:	n/a	chr21:46224943-46224961
18	USF1	chr21:46224825-46225097	SK-N-SH_RA	brain:	n/a	n/a
19	POLR2A	chr21:46223272-46225438	GM12892	blood:	n/a	n/a
20	POLR2A	chr21:46224055-46226000	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr21:46223810-46225354	A549	lung:	n/a	n/a
22	POLR2A	chr21:46224671-46224945	HepG2	liver:	n/a	n/a
23	POLR2A	chr21:46221076-46225970	GM12878	blood:	n/a	n/a
24	POLR2A	chr21:46222351-46225533	GM12878	blood:	n/a	n/a
25	POLR2A	chr21:46221326-46226084	HepG2	liver:	n/a	n/a
26	POLR2A	chr21:46224685-46225602	GM12892	blood:	n/a	n/a
27	POLR2A	chr21:46223661-46225367	HepG2	liver:	n/a	n/a
28	POLR2A	chr21:46224046-46225500	MCF-7	breast:	n/a	n/a
29	POLR2A	chr21:46221340-46225636	GM12892	blood:	n/a	n/a
30	POLR2A	chr21:46220647-46225708	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr21:46220865-46226037	GM12891	blood:	n/a	n/a
32	EP300	chr21:46224525-46225909	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr21:46223376-46225822	Raji	blood:	n/a	n/a
34	USF1	chr21:46224754-46225139	SK-N-SH_RA	brain:	n/a	n/a
35	POLR2A	chr21:46224680-46225149	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr21:46223566-46225559	PFSK-1	brain:	n/a	n/a
37	EP300	chr21:46224725-46224999	SK-N-SH_RA	brain:	n/a	n/a
38	POLR2A	chr21:46222085-46225519	GM12891	blood:	n/a	n/a
39	POLR2A	chr21:46224724-46225374	PANC-1	pancreas:	n/a	n/a
40	USF2	chr21:46224378-46225347	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr21:46224847-46225179	K562	blood:	n/a	n/a
42	POLR2A	chr21:46224669-46225431	GM12891	blood:	n/a	n/a
43	POLR2A	chr21:46221550-46227421	K562	blood:	n/a	n/a
44	POLR2A	chr21:46222376-46225739	HepG2	liver:	n/a	n/a
45	POLR2A	chr21:46224783-46225414	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr21:46221486-46225982	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr21:46221077-46225480	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr21:46224345-46225590	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr21:46224167-46225495	H1-hESC	embryonic stem cell:	n/a	n/a
50	GATA2	chr21:46224674-46225086	SH-SY5Y	brain:	n/a	chr21:46224817-46224833 chr21:46224821-46224828 chr21:46224821-46224828 chr21:46224814-46224835 chr21:46224821-46224828

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46223596..46225546-chr21:46364000..46366683,2	MCF-7	breast:
2	chr21:46223675..46225793-chr21:46292285..46293975,2	MCF-7	breast:
3	chr21:46224269..46228564-chr21:46290759..46294027,4	K562	blood:
4	chr21:46223417..46225728-chr21:46304439..46306955,2	K562	blood:
5	chr21:46220930..46225769-chr21:46292170..46294469,5	K562	blood:
6	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

No data

Variant related genes	Relation type
UBE2G2	TF binding region
ENSG00000160255	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000273027	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 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
5	nsv459298	chr21:46223847-46277968	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv587813	chr21:46223847-46277968	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv913963	chr21:46223847-46277968	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46222400-46236400	Weak transcription	Small Intestine	intestine
2	chr21:46222600-46225000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr21:46222600-46226200	Weak transcription	Esophagus	oesophagus
4	chr21:46222600-46226800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr21:46222600-46234800	Weak transcription	Right Atrium	heart
6	chr21:46222600-46236400	Weak transcription	Stomach Mucosa	stomach
7	chr21:46222600-46237200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr21:46222800-46225000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr21:46222800-46225000	Weak transcription	Brain Hippocampus Middle	brain
10	chr21:46222800-46225200	Weak transcription	Fetal Brain Male	brain
11	chr21:46222800-46225200	Weak transcription	Fetal Kidney	kidney
12	chr21:46222800-46225400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr21:46222800-46226400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:46222800-46226400	Weak transcription	Gastric	stomach
15	chr21:46222800-46226600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr21:46222800-46236400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:46222800-46237200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr21:46223000-46225000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr21:46223000-46225200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr21:46223000-46225200	Weak transcription	Right Ventricle	heart
21	chr21:46223000-46225200	Weak transcription	NH-A	brain
22	chr21:46223000-46225800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr21:46223000-46226000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr21:46223000-46226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr21:46223000-46230800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr21:46223000-46230800	Strong transcription	NHEK	skin
27	chr21:46223000-46232400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:46223000-46233600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr21:46223000-46233600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:46223000-46234200	Strong transcription	Placenta	Placenta
31	chr21:46223000-46236400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr21:46223000-46236400	Strong transcription	Fetal Stomach	stomach
33	chr21:46223200-46225000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr21:46223200-46225000	Weak transcription	Fetal Muscle Leg	muscle
35	chr21:46223200-46226400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr21:46223200-46226800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:46223200-46228000	Strong transcription	HSMM	muscle
38	chr21:46223200-46230000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr21:46223200-46230600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr21:46223200-46234000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr21:46223200-46234000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr21:46223200-46234000	Strong transcription	NHLF	lung
43	chr21:46223200-46235200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:46223200-46235800	Strong transcription	Fetal Intestine Small	intestine
45	chr21:46223400-46225000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr21:46223400-46226000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr21:46223400-46226400	Weak transcription	A549	lung
48	chr21:46223400-46230400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr21:46223400-46230800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr21:46223400-46231000	Strong transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links