Variant report

Variant	rs28542431
Chromosome Location	chr21:17109450-17109451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17108742..17111248-chr21:17133909..17136883,3	K562	blood:
2	chr21:17102017..17104012-chr21:17109243..17111259,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10482874	1.00[EUR][1000 genomes]
rs11911651	1.00[EUR][1000 genomes]
rs1474736	1.00[EUR][1000 genomes]
rs16988288	1.00[EUR][1000 genomes]
rs2225401	1.00[EUR][1000 genomes]
rs2823401	1.00[EUR][1000 genomes]
rs2823409	1.00[EUR][1000 genomes]
rs2823410	1.00[EUR][1000 genomes]
rs2823437	1.00[EUR][1000 genomes]
rs2823439	1.00[EUR][1000 genomes]
rs2823442	1.00[EUR][1000 genomes]
rs2823448	1.00[EUR][1000 genomes]
rs2823450	1.00[EUR][1000 genomes]
rs28372331	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28465005	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28510398	1.00[EUR][1000 genomes]
rs28542389	1.00[EUR][1000 genomes]
rs28627638	1.00[EUR][1000 genomes]
rs57348380	1.00[EUR][1000 genomes]
rs58963354	1.00[EUR][1000 genomes]
rs61348938	1.00[EUR][1000 genomes]
rs6517555	1.00[EUR][1000 genomes]
rs7281995	1.00[EUR][1000 genomes]
rs7282463	1.00[EUR][1000 genomes]
rs73355413	1.00[AMR][1000 genomes]
rs73355433	1.00[AMR][1000 genomes]
rs73355441	1.00[EUR][1000 genomes]
rs73360907	1.00[EUR][1000 genomes]
rs73360910	1.00[EUR][1000 genomes]
rs73360912	1.00[EUR][1000 genomes]
rs73360916	1.00[EUR][1000 genomes]
rs7364033	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7510266	1.00[EUR][1000 genomes]
rs8126822	1.00[EUR][1000 genomes]
rs8127197	1.00[EUR][1000 genomes]
rs8129950	1.00[EUR][1000 genomes]
rs8130259	1.00[EUR][1000 genomes]
rs8131104	1.00[EUR][1000 genomes]
rs9305732	1.00[AMR][1000 genomes]
rs995121	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9974370	1.00[AMR][1000 genomes]
rs9974439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9974570	1.00[EUR][1000 genomes]
rs9977583	1.00[EUR][1000 genomes]
rs9977671	1.00[EUR][1000 genomes]
rs9978819	1.00[EUR][1000 genomes]
rs9979887	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9980143	1.00[EUR][1000 genomes]
rs9980755	1.00[AMR][1000 genomes]
rs9981034	1.00[EUR][1000 genomes]
rs9981661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9981989	1.00[AMR][1000 genomes]
rs9982635	1.00[EUR][1000 genomes]
rs9983023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9983852	1.00[EUR][1000 genomes]
rs9983961	1.00[EUR][1000 genomes]
rs9984675	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9984939	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv2830057	chr21:16960590-17113148	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17103200-17114400	Weak transcription	Spleen	Spleen
2	chr21:17103400-17114400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:17103800-17114400	Weak transcription	Lung	lung
4	chr21:17103800-17115000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:17104000-17114600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:17104000-17114600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr21:17104200-17110800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
9	chr21:17104600-17111800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr21:17104600-17113000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr21:17104600-17114600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr21:17104600-17123400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr21:17104800-17111400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:17104800-17115000	Weak transcription	Fetal Muscle Leg	muscle
15	chr21:17105000-17114000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr21:17105400-17110800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr21:17105400-17111600	Weak transcription	Brain Anterior Caudate	brain
18	chr21:17105400-17111600	Weak transcription	Esophagus	oesophagus
19	chr21:17105400-17111800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr21:17105400-17112000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:17105400-17112200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:17105400-17112200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr21:17105400-17112400	Weak transcription	Brain Hippocampus Middle	brain
24	chr21:17105400-17113200	Weak transcription	NH-A	brain
25	chr21:17105400-17113600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr21:17105400-17113800	Weak transcription	HSMMtube	muscle
27	chr21:17105400-17114000	Weak transcription	HMEC	breast
28	chr21:17105400-17114400	Weak transcription	Brain Germinal Matrix	brain
29	chr21:17105400-17114800	Weak transcription	Fetal Stomach	stomach
30	chr21:17105400-17115000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr21:17105400-17115200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr21:17105400-17119400	Weak transcription	Brain Angular Gyrus	brain
33	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
34	chr21:17105800-17110800	Weak transcription	Fetal Intestine Large	intestine
35	chr21:17105800-17114600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr21:17106000-17114400	Weak transcription	Gastric	stomach
37	chr21:17106000-17114600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr21:17106200-17114800	Weak transcription	Fetal Thymus	thymus
39	chr21:17106400-17113000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr21:17106400-17114800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr21:17106400-17115200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr21:17106600-17110600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr21:17106600-17110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr21:17106600-17112000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr21:17106600-17112400	Enhancers	Primary T cells from cord blood	blood
46	chr21:17106600-17113600	Weak transcription	NHEK	skin
47	chr21:17106600-17114800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr21:17106600-17116600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr21:17106800-17115200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr21:17107400-17109800	Enhancers	HUES48 Cell Line	embryonic stem cell

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