Variant report

Variant	rs28725201
Chromosome Location	chr21:17129839-17129840
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	chr21:17128179..17129872-chr21:17129945..17132364,2	K562	blood:
2	chr21:17127290..17130073-chr21:17133451..17135040,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11910884	0.83[ASN][1000 genomes]
rs11911814	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1989381	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2205585	0.84[ASN][1000 genomes]
rs2223176	0.84[ASN][1000 genomes]
rs2245574	0.83[ASN][1000 genomes]
rs2823469	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823470	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823472	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823476	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823482	0.88[ASN][1000 genomes]
rs2823489	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2823493	0.84[ASN][1000 genomes]
rs2823495	0.84[ASN][1000 genomes]
rs2823496	0.84[ASN][1000 genomes]
rs2823497	0.83[ASN][1000 genomes]
rs6517609	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517611	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6517613	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517648	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6517652	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs722887	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7279157	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7279170	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7283707	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8127158	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8134327	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941829	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9974210	0.81[ASN][1000 genomes]
rs9977000	0.83[ASN][1000 genomes]
rs9981766	0.83[ASN][1000 genomes]
rs9982083	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9982479	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983458	0.87[EUR][1000 genomes];0.83[ASN][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	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
9	esv275197	chr21:17123855-17130358	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
2	chr21:17115200-17130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
4	chr21:17115600-17133400	Weak transcription	Dnd41	blood
5	chr21:17115600-17139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr21:17116200-17139400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr21:17116600-17145400	Weak transcription	Esophagus	oesophagus
8	chr21:17122600-17142800	Weak transcription	Hela-S3	cervix
9	chr21:17123400-17130200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr21:17123600-17133000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr21:17124800-17130200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr21:17124800-17130200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr21:17125800-17133600	Weak transcription	Lung	lung
14	chr21:17125800-17153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:17126200-17134600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr21:17126600-17130200	ZNF genes & repeats	GM12878-XiMat	blood
17	chr21:17126600-17131200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr21:17126600-17137200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr21:17126800-17133600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:17126800-17147600	Weak transcription	Placenta	Placenta
21	chr21:17127000-17130400	Weak transcription	Aorta	Aorta
22	chr21:17127000-17131800	Weak transcription	Right Atrium	heart
23	chr21:17127000-17132000	Weak transcription	Fetal Heart	heart
24	chr21:17127000-17133400	Weak transcription	Pancreas	Pancrea
25	chr21:17127000-17147400	Weak transcription	HSMMtube	muscle
26	chr21:17127000-17152800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr21:17127200-17131600	Weak transcription	Right Ventricle	heart
28	chr21:17127200-17132000	Weak transcription	Psoas Muscle	Psoas
29	chr21:17127200-17132400	Weak transcription	Spleen	Spleen
30	chr21:17127200-17139400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr21:17127200-17140800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr21:17127200-17153400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr21:17127400-17133800	Weak transcription	Fetal Lung	lung
34	chr21:17127400-17146200	Weak transcription	NHDF-Ad	bronchial
35	chr21:17127400-17147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr21:17127400-17153400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr21:17127600-17130000	Weak transcription	Fetal Intestine Small	intestine
38	chr21:17127600-17145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr21:17127800-17131800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr21:17127800-17139400	Weak transcription	Fetal Kidney	kidney
41	chr21:17127800-17141600	Weak transcription	HMEC	breast
42	chr21:17127800-17152800	Weak transcription	Fetal Intestine Large	intestine
43	chr21:17128000-17130400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr21:17128000-17131600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr21:17128000-17132000	Weak transcription	Stomach Mucosa	stomach
46	chr21:17128000-17132400	Weak transcription	Colon Smooth Muscle	Colon
47	chr21:17128000-17132800	Weak transcription	Adipose Nuclei	Adipose
48	chr21:17128000-17135200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr21:17128000-17139400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr21:17128200-17132400	Weak transcription	Liver	Liver

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