Variant report

Variant	nsv933128
Chromosome Location	chr21:47407024-47407402
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47407254..47409991-chr21:47416573..47418228,3	K562	blood:
2	chr21:47407254..47409991-chr21:47416573..47418228,2	K562	blood:
3	chr21:47399588..47401782-chr21:47405993..47408923,2	MCF-7	breast:
4	chr21:47401629..47403752-chr21:47406521..47408992,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCBP3-2	chr21:47407023-47407433	NONHSAT083006

Variant related genes	Relation type
ENSG00000142156	chromatin interactions

Extended variants
information (count: 32 )
Associated
traits (count: 36 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200557184	chr21:47407027-47407028	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs370725821	chr21:47407028-47407029	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs373438206	chr21:47407048-47407049	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs377587209	chr21:47407049-47407050	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs147612667	chr21:47407071-47407072	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs142102852	chr21:47407077-47407078	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs557153744	chr21:47407078-47407079	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs374896651	chr21:47407103-47407104	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs576435781	chr21:47407104-47407105	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs187649260	chr21:47407117-47407118	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs367669227	chr21:47407131-47407132	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs199802096	chr21:47407132-47407133	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs201136430	chr21:47407135-47407136	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs559795661	chr21:47407155-47407156	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs374034428	chr21:47407181-47407182	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs533725138	chr21:47407185-47407186	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs558687936	chr21:47407211-47407212	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs113013628	chr21:47407214-47407215	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs192616290	chr21:47407215-47407216	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs531033030	chr21:47407251-47407252	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs548634821	chr21:47407294-47407295	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs567032530	chr21:47407295-47407296	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs534274493	chr21:47407303-47407304	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs184225117	chr21:47407319-47407320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs571435860	chr21:47407339-47407340	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs374517899	chr21:47407340-47407341	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs62215498	chr21:47407362-47407363	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs556996397	chr21:47407363-47407364	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs544502169	chr21:47407365-47407366	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs372618333	chr21:47407371-47407372	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs144843800	chr21:47407395-47407396	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs573196191	chr21:47407400-47407401	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47401200-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr21:47402800-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr21:47403200-47414600	Weak transcription	Brain Substantia Nigra	brain
4	chr21:47403200-47415200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:47403200-47424600	Weak transcription	Small Intestine	intestine
6	chr21:47403200-47425000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr21:47403600-47409600	Weak transcription	Fetal Thymus	thymus
8	chr21:47403600-47414800	Strong transcription	Fetal Intestine Small	intestine
9	chr21:47404000-47407600	Genic enhancers	Placenta	Placenta
10	chr21:47404000-47424200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr21:47404000-47424600	Strong transcription	Aorta	Aorta
12	chr21:47404200-47407400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr21:47404200-47407600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:47404200-47407600	Genic enhancers	Ovary	ovary
15	chr21:47404200-47407600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
16	chr21:47404200-47407800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr21:47404200-47407800	Strong transcription	Brain Germinal Matrix	brain
18	chr21:47404200-47414400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr21:47404200-47425200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:47404200-47425200	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr21:47404400-47407200	Strong transcription	Gastric	stomach
22	chr21:47404400-47407600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr21:47404400-47407600	Genic enhancers	Rectal Smooth Muscle	rectum
24	chr21:47404400-47409600	Weak transcription	Right Atrium	heart
25	chr21:47404400-47414600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:47404400-47419200	Strong transcription	Left Ventricle	heart
27	chr21:47404600-47407600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr21:47404600-47408600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr21:47404800-47407200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr21:47404800-47407400	Strong transcription	HSMM	muscle
31	chr21:47405000-47407400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr21:47405000-47407600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr21:47405000-47407600	Genic enhancers	NH-A	brain
34	chr21:47405000-47407800	Strong transcription	Fetal Lung	lung
35	chr21:47405000-47409200	Weak transcription	Brain Angular Gyrus	brain
36	chr21:47405000-47414600	Weak transcription	Fetal Kidney	kidney
37	chr21:47405000-47417400	Weak transcription	Stomach Mucosa	stomach
38	chr21:47405000-47419400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr21:47405000-47423800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr21:47405000-47425400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr21:47405200-47407200	Strong transcription	Pancreas	Pancrea
42	chr21:47405200-47407400	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr21:47405200-47407600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr21:47405200-47407600	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr21:47405200-47425400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr21:47405200-47425400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr21:47405200-47425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr21:47405400-47407200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr21:47405400-47407600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr21:47405400-47407600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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