Variant report

Variant	rs2838820
Chromosome Location	chr21:46646005-46646006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46494100..46496574-chr21:46644222..46646610,2	K562	blood:
2	chr21:46645128..46646956-chr21:46675006..46677594,2	MCF-7	breast:
3	chr21:46644635..46649401-chr21:46653595..46657283,5	MCF-7	breast:
4	chr21:46495879..46498410-chr21:46645680..46647627,2	K562	blood:
5	chr21:46617772..46620872-chr21:46645062..46648136,3	K562	blood:

Variant related genes	Relation type
ENSG00000182586	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1051367	0.81[EUR][1000 genomes]
rs11701929	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2253763	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2838797	0.84[MEX][hapmap]
rs2838818	0.82[ASW][hapmap];0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs381466	0.88[MEX][hapmap]
rs386762	0.88[MEX][hapmap]
rs446158	0.96[MEX][hapmap]
rs9637192	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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
7	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv587841	chr21:46619840-46647078	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv913999	chr21:46636844-46765251	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	43 gene(s)	inside rSNPs	diseases
19	nsv587842	chr21:46641017-46670752	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838820	C21orf58	cis	parietal	SCAN
rs2838820	C21orf122	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46610800-46647800	Weak transcription	Brain Angular Gyrus	brain
2	chr21:46632600-46647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:46637800-46668600	Weak transcription	Right Atrium	heart
4	chr21:46638400-46646400	Weak transcription	Fetal Intestine Large	intestine
5	chr21:46638600-46646600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:46639800-46646400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:46639800-46648000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr21:46641000-46648000	Weak transcription	Fetal Brain Male	brain
9	chr21:46641600-46648400	Weak transcription	Brain Substantia Nigra	brain
10	chr21:46642000-46648800	Weak transcription	Primary B cells from cord blood	blood
11	chr21:46642200-46648000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr21:46642400-46649200	Weak transcription	Fetal Intestine Small	intestine
13	chr21:46642800-46646200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr21:46642800-46647000	Weak transcription	Dnd41	blood
15	chr21:46642800-46647800	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:46643600-46646200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr21:46643600-46646600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr21:46643600-46649600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr21:46643800-46646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:46643800-46647000	Enhancers	Fetal Thymus	thymus
21	chr21:46643800-46647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr21:46643800-46647800	Weak transcription	Brain Anterior Caudate	brain
23	chr21:46643800-46648000	Weak transcription	Esophagus	oesophagus
24	chr21:46643800-46648800	Weak transcription	Left Ventricle	heart
25	chr21:46643800-46664600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr21:46644000-46646400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr21:46644000-46646400	Weak transcription	Gastric	stomach
28	chr21:46644000-46646600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr21:46644000-46646800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr21:46644000-46646800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr21:46644000-46647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr21:46644000-46647000	Weak transcription	Adipose Nuclei	Adipose
33	chr21:46644000-46647400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr21:46644000-46647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr21:46644000-46647800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr21:46644000-46647800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr21:46644000-46647800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr21:46644000-46648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr21:46644000-46648000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr21:46644000-46648200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr21:46644000-46652200	Weak transcription	Pancreas	Pancrea
42	chr21:46644200-46647600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr21:46644200-46648000	Weak transcription	Colon Smooth Muscle	Colon
44	chr21:46644200-46648400	Weak transcription	Fetal Muscle Leg	muscle
45	chr21:46644200-46648800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr21:46644200-46649000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr21:46644200-46649200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr21:46644400-46646800	Weak transcription	Fetal Stomach	stomach
49	chr21:46644400-46647400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr21:46644400-46648400	Weak transcription	Lung	lung

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