Variant report

Variant	rs2403873
Chromosome Location	chr21:16420310-16420311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:16413029..16416695-chr21:16417733..16422719,4	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1041404	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13052454	0.92[ASN][1000 genomes]
rs2026848	0.92[ASN][1000 genomes]
rs2142216	0.99[ASN][1000 genomes]
rs2142218	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2142219	0.92[ASN][1000 genomes]
rs2223041	0.86[AFR][1000 genomes]
rs2248589	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2403874	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2823017	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2823022	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2823027	0.98[ASN][1000 genomes]
rs2823029	0.94[ASN][1000 genomes]
rs4356736	1.00[ASN][1000 genomes]
rs8132398	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8133012	0.95[ASN][1000 genomes]
rs8133792	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060151	chr21:16295713-16435497	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv544378	chr21:16295713-16435497	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer 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	5 gene(s)	inside rSNPs	diseases
3	nsv834048	chr21:16324481-16489570	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv913411	chr21:16380025-16424421	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv587050	chr21:16413682-16462268	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16364800-16423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:16374800-16423200	Weak transcription	Colonic Mucosa	Colon
3	chr21:16400000-16423200	Weak transcription	Fetal Stomach	stomach
4	chr21:16400200-16423200	Weak transcription	Brain Hippocampus Middle	brain
5	chr21:16400800-16423000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr21:16401400-16423000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr21:16401600-16423000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr21:16401600-16426400	Weak transcription	HUVEC	blood vessel
9	chr21:16402400-16420600	Weak transcription	Brain Angular Gyrus	brain
10	chr21:16403600-16423200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:16406800-16421000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr21:16407000-16420600	Weak transcription	Thymus	Thymus
13	chr21:16407000-16422000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr21:16407000-16423400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr21:16407400-16420600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr21:16407400-16421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr21:16407400-16422000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr21:16407400-16422600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr21:16407400-16422600	Weak transcription	Brain Anterior Caudate	brain
20	chr21:16407400-16425600	Weak transcription	NHDF-Ad	bronchial
21	chr21:16407400-16431200	Weak transcription	NHEK	skin
22	chr21:16408600-16425800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr21:16408800-16423800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr21:16410000-16422000	Weak transcription	Colon Smooth Muscle	Colon
25	chr21:16410400-16426400	Weak transcription	HMEC	breast
26	chr21:16410600-16423400	Weak transcription	Fetal Brain Male	brain
27	chr21:16413600-16421800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr21:16413600-16423000	Weak transcription	Brain Germinal Matrix	brain
29	chr21:16414400-16427200	Weak transcription	Aorta	Aorta
30	chr21:16414600-16421000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:16415000-16421600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr21:16415200-16422600	Weak transcription	Fetal Kidney	kidney
33	chr21:16415200-16423000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr21:16415200-16423200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:16415200-16424000	Weak transcription	HSMMtube	muscle
36	chr21:16415200-16431200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr21:16415400-16420400	Weak transcription	Adipose Nuclei	Adipose
38	chr21:16415400-16420400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr21:16415400-16422600	Weak transcription	Fetal Lung	lung
40	chr21:16415400-16422800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr21:16415400-16423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr21:16415400-16423000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr21:16415400-16423000	Weak transcription	Esophagus	oesophagus
44	chr21:16415400-16423000	Weak transcription	Left Ventricle	heart
45	chr21:16415400-16423000	Weak transcription	Ovary	ovary
46	chr21:16415400-16423000	Weak transcription	Pancreas	Pancrea
47	chr21:16415400-16423000	Weak transcription	Dnd41	blood
48	chr21:16415400-16423600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr21:16415400-16427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr21:16415400-16429600	Weak transcription	Fetal Muscle Trunk	muscle

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