Variant report

Variant	esv3413597
Chromosome Location	chr21:47404755-47405077
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	HDAC2	chr21:47404902-47405181	K562	blood:	n/a	n/a
2	POLR2A	chr21:47404867-47405309	U87	brain:	n/a	n/a
3	SIX5	chr21:47404713-47404887	K562	blood:	n/a	n/a
4	ZNF143	chr21:47404675-47404991	GM12878	blood:	n/a	n/a
5	ZNF143	chr21:47404486-47405074	K562	blood:	n/a	n/a
6	ZNF143	chr21:47404646-47404906	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr21:47404505-47405434	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50057880..50060234-chr21:47402833..47404920,2	MCF-7	breast:
2	chr21:47402572..47405446-chr21:47518065..47519578,2	MCF-7	breast:
3	chr21:47334656..47336650-chr21:47402926..47405175,2	MCF-7	breast:

Variant related genes	Relation type
COL6A1	TF binding region
ENSG00000142173	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 36 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566770967	chr21:47404769-47404770	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs201918455	chr21:47404795-47404796	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs111220493	chr21:47404796-47404797	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs557357418	chr21:47404808-47404809	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs183152208	chr21:47404815-47404816	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs575847021	chr21:47404818-47404819	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs564350257	chr21:47404838-47404839	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs559167640	chr21:47404858-47404859	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs181684258	chr21:47404863-47404864	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs563248227	chr21:47404864-47404865	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs186026448	chr21:47404868-47404869	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs574091800	chr21:47404894-47404895	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs549540669	chr21:47404902-47404903	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs553191105	chr21:47404913-47404914	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs557384481	chr21:47404920-47404921	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs569254812	chr21:47404921-47404922	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs367594568	chr21:47404957-47404958	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs62652572	chr21:47404981-47404982	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs62652573	chr21:47404987-47404988	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs554582496	chr21:47404993-47404994	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs9754024	chr21:47405021-47405022	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs139463824	chr21:47405033-47405034	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs553238039	chr21:47405036-47405037	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs568455135	chr21:47405044-47405045	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs577335977	chr21:47405045-47405046	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs189616053	chr21:47405048-47405049	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs200995260	chr21:47405056-47405057	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs562557999	chr21:47405064-47405065	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs574634056	chr21:47405076-47405077	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	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:117 , 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	chr21:47402200-47406200	Transcr. at gene 5' and 3'	NHLF	lung
3	chr21:47402400-47405400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:47402600-47405400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr21:47402600-47405600	Transcr. at gene 5' and 3'	Osteobl	bone
6	chr21:47402800-47404800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr21:47402800-47406000	Weak transcription	Liver	Liver
8	chr21:47402800-47406000	Weak transcription	Brain Hippocampus Middle	brain
9	chr21:47402800-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:47403200-47405000	Weak transcription	Brain Anterior Caudate	brain
11	chr21:47403200-47414600	Weak transcription	Brain Substantia Nigra	brain
12	chr21:47403200-47415200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:47403200-47424600	Weak transcription	Small Intestine	intestine
14	chr21:47403200-47425000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr21:47403400-47405400	Weak transcription	Fetal Brain Female	brain
16	chr21:47403400-47406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr21:47403400-47406000	Genic enhancers	Spleen	Spleen
18	chr21:47403600-47405000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:47403600-47405200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr21:47403600-47405800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr21:47403600-47406800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr21:47403600-47409600	Weak transcription	Fetal Thymus	thymus
23	chr21:47403600-47414800	Strong transcription	Fetal Intestine Small	intestine
24	chr21:47403800-47405600	Genic enhancers	Fetal Muscle Leg	muscle
25	chr21:47403800-47405600	Genic enhancers	Fetal Stomach	stomach
26	chr21:47404000-47404800	Bivalent Enhancer	K562	blood
27	chr21:47404000-47405000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
28	chr21:47404000-47405200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr21:47404000-47405600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
30	chr21:47404000-47406400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
31	chr21:47404000-47407600	Genic enhancers	Placenta	Placenta
32	chr21:47404000-47424200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr21:47404000-47424600	Strong transcription	Aorta	Aorta
34	chr21:47404200-47404800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr21:47404200-47405000	Transcr. at gene 5' and 3'	NH-A	brain
36	chr21:47404200-47405400	Strong transcription	Esophagus	oesophagus
37	chr21:47404200-47405600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr21:47404200-47405800	Strong transcription	HSMMtube	muscle
39	chr21:47404200-47406200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
40	chr21:47404200-47406200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
41	chr21:47404200-47406600	Strong transcription	Right Ventricle	heart
42	chr21:47404200-47407400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:47404200-47407600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr21:47404200-47407600	Genic enhancers	Ovary	ovary
45	chr21:47404200-47407600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
46	chr21:47404200-47407800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr21:47404200-47407800	Strong transcription	Brain Germinal Matrix	brain
48	chr21:47404200-47414400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr21:47404200-47425200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr21:47404200-47425200	Strong transcription	Muscle Satellite Cultured Cells	--

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