Variant report

Variant	esv3390518
Chromosome Location	chr21:47329274-47330722
allele	n/a
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	CTCF	chr21:47329478-47329550	Lung_OC	lung:	n/a	n/a
2	HDAC2	chr21:47330363-47330862	MCF-7	breast:	n/a	chr21:47330445-47330459
3	MYC	chr21:47330617-47330699	MCF-7	breast:	n/a	n/a
4	NFIC	chr21:47330252-47330931	ECC-1	luminal epithelium:	n/a	chr21:47330583-47330599 chr21:47330581-47330597 chr21:47330581-47330598 chr21:47330582-47330599
5	NFIC	chr21:47330211-47330839	SK-N-SH	brain:	n/a	chr21:47330583-47330599 chr21:47330581-47330597 chr21:47330581-47330598 chr21:47330582-47330599
6	NFIC	chr21:47330189-47330813	ECC-1	luminal epithelium:	n/a	chr21:47330583-47330599 chr21:47330581-47330597 chr21:47330581-47330598 chr21:47330582-47330599
7	SRF	chr21:47330026-47330584	MCF-7	breast:	n/a	n/a
8	USF1	chr21:47330098-47330276	SK-N-SH_RA	brain:	n/a	n/a
9	USF1	chr21:47330092-47330357	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47324736..47327193-chr21:47327348..47329802,3	K562	blood:
2	chr21:47329285..47331470-chr21:47342066..47344987,2	MCF-7	breast:
3	chr21:47253579..47256281-chr21:47326370..47329354,2	K562	blood:
4	chr21:47328644..47331016-chr21:47340908..47343121,3	MCF-7	breast:
5	chr21:47318888..47321827-chr21:47328391..47331106,3	MCF-7	breast:
6	chr21:47329095..47331174-chr21:47334966..47337510,2	MCF-7	breast:

Variant related genes	Relation type
PCBP3	TF binding region
ENSG00000183570	chromatin interactions

Extended variants
information (count: 83 )
Associated
traits (count: 36 )

Variant overlapped rSNPs/rCNVs (count:83 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2277812	chr21:47329352-47329353	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs201330830	chr21:47329364-47329365	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs367782910	chr21:47329391-47329392	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs201370119	chr21:47329419-47329420	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs371466860	chr21:47329420-47329421	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs538625178	chr21:47329423-47329424	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs375755127	chr21:47329425-47329426	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs556720525	chr21:47329426-47329427	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs200185743	chr21:47329427-47329428	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs536551516	chr21:47329431-47329432	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs374292013	chr21:47329432-47329433	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs377156061	chr21:47329443-47329444	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs369550936	chr21:47329450-47329451	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs373450618	chr21:47329451-47329452	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs540470185	chr21:47329461-47329462	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs559779318	chr21:47329566-47329567	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs569258171	chr21:47329588-47329589	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs545376900	chr21:47329590-47329591	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs376991074	chr21:47329601-47329602	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs187340968	chr21:47329625-47329626	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs531063865	chr21:47329651-47329652	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs536604557	chr21:47329673-47329674	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs79874805	chr21:47329682-47329683	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs2507741	chr21:47329697-47329698	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs376651490	chr21:47329705-47329706	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs192693604	chr21:47329715-47329716	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs2507742	chr21:47329727-47329728	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs549289630	chr21:47329738-47329739	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs561278880	chr21:47329739-47329740	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs528638819	chr21:47329740-47329741	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs113313099	chr21:47329759-47329760	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs113572552	chr21:47329760-47329761	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs71185168	chr21:47329764-47329765	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs546924596	chr21:47329765-47329766	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs571310582	chr21:47329766-47329767	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs184529209	chr21:47329866-47329867	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs118155748	chr21:47329930-47329931	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs115006847	chr21:47329931-47329932	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs189505503	chr21:47329954-47329955	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs554890600	chr21:47329969-47329970	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs573204231	chr21:47329971-47329972	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs180747237	chr21:47329992-47329993	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs79743314	chr21:47330008-47330009	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs113561786	chr21:47330018-47330019	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs189711856	chr21:47330028-47330029	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs181199020	chr21:47330037-47330038	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs34369577	chr21:47330052-47330053	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs572942376	chr21:47330055-47330056	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs71324454	chr21:47330070-47330071	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs35773702	chr21:47330075-47330076	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:36)

Disease	PMID	Source
Down syndrome	17576883	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Autism	18414403	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Breast cancer	17899364	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Cholangiocarcinoma	16830362	CNVD
Down syndrome	17334655	CNVD
Neuroticism	17667963	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Autoimmune polyendocrine syndrome	18200029	CNVD
Prostate cancer	19363497	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Olfactory neuroblastoma	18408657	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Multiple myeloma	16616336	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47308000-47343000	Weak transcription	Right Atrium	heart
2	chr21:47313200-47335600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr21:47314400-47330200	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:47314600-47330200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr21:47315000-47330200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr21:47315200-47330200	Weak transcription	Adipose Nuclei	Adipose
7	chr21:47320200-47330200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr21:47321800-47333000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:47321800-47337800	Weak transcription	Primary T cells from cord blood	blood
10	chr21:47322200-47335200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:47322400-47330200	Weak transcription	Right Ventricle	heart
12	chr21:47325000-47331400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr21:47325600-47335600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:47326000-47330800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr21:47326200-47333000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:47327000-47335600	Weak transcription	Fetal Thymus	thymus
17	chr21:47327200-47331200	Enhancers	Fetal Heart	heart
18	chr21:47328400-47329600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr21:47328400-47330200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr21:47328400-47331200	Enhancers	Spleen	Spleen
21	chr21:47328600-47329400	ZNF genes & repeats	Thymus	Thymus
22	chr21:47328800-47329600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr21:47328800-47330200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr21:47329000-47329600	Enhancers	Brain Germinal Matrix	brain
25	chr21:47329000-47330400	Enhancers	Esophagus	oesophagus
26	chr21:47329000-47331000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr21:47329200-47329600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr21:47329200-47329600	Enhancers	Brain Substantia Nigra	brain
29	chr21:47329200-47329800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr21:47329200-47330200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr21:47329200-47331200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr21:47329400-47334400	Strong transcription	Thymus	Thymus
33	chr21:47329600-47330000	Weak transcription	Brain Germinal Matrix	brain
34	chr21:47329600-47330000	Weak transcription	Brain Substantia Nigra	brain
35	chr21:47329600-47330200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr21:47329600-47330200	Enhancers	Fetal Muscle Trunk	muscle
37	chr21:47329600-47333400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr21:47330000-47330800	Enhancers	Brain Germinal Matrix	brain
39	chr21:47330000-47331000	Enhancers	Brain Substantia Nigra	brain
40	chr21:47330200-47330400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr21:47330200-47330400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr21:47330200-47330400	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr21:47330200-47330400	Enhancers	Right Ventricle	heart
44	chr21:47330200-47330600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr21:47330200-47330600	Enhancers	Adipose Nuclei	Adipose
46	chr21:47330200-47330600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:47330200-47330600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr21:47330200-47330600	Enhancers	Fetal Lung	lung
49	chr21:47330200-47330600	Enhancers	Fetal Muscle Leg	muscle
50	chr21:47330200-47330600	Enhancers	HMEC	breast

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