Variant report

Variant	esv3428412
Chromosome Location	chr21:47416979-47417150
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47416940-47417296	U87	brain:	n/a	n/a
2	POLR2A	chr21:47416934-47417319	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47416853..47418859-chr21:47421399..47424312,2	K562	blood:
2	chr21:47407254..47409991-chr21:47416573..47418228,3	K562	blood:
3	chr21:47407254..47409991-chr21:47416573..47418228,2	K562	blood:
4	chr21:47415907..47418450-chr21:47418722..47421230,2	MCF-7	breast:
5	chr21:47410997..47412945-chr21:47415697..47417959,2	MCF-7	breast:

No data

Variant related genes	Relation type
COL6A1	TF binding region
ENSG00000142156	chromatin interactions

Extended variants
information (count: 18 )
Associated
traits (count: 36 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs188238761	chr21:47416993-47416994	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs536894938	chr21:47416995-47416996	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs554357145	chr21:47417000-47417001	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs573008650	chr21:47417014-47417015	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs558559633	chr21:47417026-47417027	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs576928795	chr21:47417032-47417033	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs544138299	chr21:47417037-47417038	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs112124422	chr21:47417051-47417052	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs562805451	chr21:47417052-47417053	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs574545284	chr21:47417063-47417064	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs542049728	chr21:47417068-47417069	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs561033384	chr21:47417077-47417078	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs115807593	chr21:47417089-47417090	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs546713446	chr21:47417093-47417094	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs564904594	chr21:47417107-47417108	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs79779816	chr21:47417114-47417115	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs146034711	chr21:47417125-47417126	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs148786363	chr21:47417148-47417149	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	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:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47403200-47424600	Weak transcription	Small Intestine	intestine
2	chr21:47403200-47425000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr21:47404000-47424200	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr21:47404000-47424600	Strong transcription	Aorta	Aorta
5	chr21:47404200-47425200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr21:47404200-47425200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr21:47404400-47419200	Strong transcription	Left Ventricle	heart
8	chr21:47405000-47417400	Weak transcription	Stomach Mucosa	stomach
9	chr21:47405000-47419400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:47405000-47423800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr21:47405000-47425400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr21:47405200-47425400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr21:47405200-47425400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr21:47405200-47425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:47405400-47423800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:47405400-47424800	Strong transcription	Fetal Brain Female	brain
17	chr21:47405400-47425200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr21:47405600-47419800	Strong transcription	Fetal Stomach	stomach
19	chr21:47405600-47423000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr21:47406400-47421400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr21:47406600-47425400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr21:47407600-47425000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr21:47408400-47425800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr21:47408600-47419800	Strong transcription	Brain Germinal Matrix	brain
25	chr21:47408800-47417800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr21:47409000-47425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr21:47409200-47425000	Strong transcription	Ovary	ovary
28	chr21:47409400-47419400	Strong transcription	Gastric	stomach
29	chr21:47409800-47426600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr21:47410000-47422600	Weak transcription	Liver	Liver
31	chr21:47411200-47432800	Weak transcription	Right Atrium	heart
32	chr21:47412400-47423000	Strong transcription	Colonic Mucosa	Colon
33	chr21:47412400-47426400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr21:47412600-47422400	Weak transcription	Brain Hippocampus Middle	brain
35	chr21:47412600-47425800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr21:47413400-47417000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:47413600-47420200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr21:47413800-47425200	Strong transcription	NHLF	lung
39	chr21:47414000-47421200	Strong transcription	Spleen	Spleen
40	chr21:47414200-47424800	Strong transcription	Right Ventricle	heart
41	chr21:47414400-47417600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr21:47414400-47418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr21:47414600-47421200	Strong transcription	Placenta	Placenta
44	chr21:47414800-47417200	Weak transcription	Brain Substantia Nigra	brain
45	chr21:47414800-47425200	Strong transcription	Osteobl	bone
46	chr21:47415000-47417400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr21:47415200-47417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr21:47415200-47425200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:47415400-47417200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr21:47415400-47418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links