Variant report

Variant	rs56666611
Chromosome Location	chr21:17131763-17131764
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:17126721..17128269-chr21:17130491..17133281,2	MCF-7	breast:
2	chr21:17125584..17127953-chr21:17130378..17132537,2	K562	blood:
3	chr21:17131546..17134772-chr21:17136356..17138734,3	MCF-7	breast:
4	chr21:17128179..17129872-chr21:17129945..17132364,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10482875	0.81[ASN][1000 genomes]
rs10482876	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11910884	0.84[EUR][1000 genomes]
rs1543299	0.86[EUR][1000 genomes]
rs17241395	0.87[ASN][1000 genomes]
rs17241409	0.95[EUR][1000 genomes]
rs17241416	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17241423	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17241430	0.95[EUR][1000 genomes]
rs17241444	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241460	0.80[EUR][1000 genomes]
rs17241481	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17275511	0.82[EUR][1000 genomes]
rs17307120	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17307170	0.97[EUR][1000 genomes]
rs17307176	0.82[EUR][1000 genomes]
rs17307190	0.80[EUR][1000 genomes]
rs17307197	0.80[EUR][1000 genomes]
rs17307204	0.80[EUR][1000 genomes]
rs2205585	0.84[EUR][1000 genomes]
rs2205588	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2223176	0.84[EUR][1000 genomes]
rs2242676	0.95[EUR][1000 genomes]
rs2242680	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242681	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2245574	0.81[EUR][1000 genomes]
rs2404000	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823462	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823463	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823471	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823478	0.95[EUR][1000 genomes]
rs2823481	0.98[ASN][1000 genomes]
rs2823483	0.98[ASN][1000 genomes]
rs2823484	0.98[ASN][1000 genomes]
rs2823491	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823493	0.84[EUR][1000 genomes]
rs2823495	0.84[EUR][1000 genomes]
rs2823496	0.84[EUR][1000 genomes]
rs2823497	0.81[EUR][1000 genomes]
rs2823498	0.92[ASN][1000 genomes]
rs2823499	0.82[EUR][1000 genomes]
rs2823505	0.82[EUR][1000 genomes]
rs28627435	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787577	0.82[EUR][1000 genomes]
rs4580465	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56299770	0.88[EUR][1000 genomes]
rs56333224	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56410772	0.89[EUR][1000 genomes]
rs57733106	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59084861	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60191002	0.88[EUR][1000 genomes]
rs60529604	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517675	0.82[EUR][1000 genomes]
rs7277807	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7278428	0.81[ASN][1000 genomes]
rs7281511	0.82[EUR][1000 genomes]
rs7282314	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283764	0.88[EUR][1000 genomes]
rs73181987	0.88[EUR][1000 genomes]
rs73346766	0.82[EUR][1000 genomes]
rs73355479	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73357260	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73892510	0.87[ASN][1000 genomes]
rs8128766	0.82[EUR][1000 genomes]
rs8133079	0.80[EUR][1000 genomes]
rs9974210	0.82[EUR][1000 genomes]
rs9976815	0.81[EUR][1000 genomes]
rs9977000	0.81[EUR][1000 genomes]
rs9981766	0.84[EUR][1000 genomes]
rs9983248	0.82[EUR][1000 genomes]
rs9983385	0.82[EUR][1000 genomes]
rs9983858	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

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	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
3	chr21:17115600-17133400	Weak transcription	Dnd41	blood
4	chr21:17115600-17139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr21:17116200-17139400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr21:17116600-17145400	Weak transcription	Esophagus	oesophagus
7	chr21:17122600-17142800	Weak transcription	Hela-S3	cervix
8	chr21:17123600-17133000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr21:17125800-17133600	Weak transcription	Lung	lung
10	chr21:17125800-17153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:17126200-17134600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr21:17126600-17137200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr21:17126800-17133600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:17126800-17147600	Weak transcription	Placenta	Placenta
15	chr21:17127000-17131800	Weak transcription	Right Atrium	heart
16	chr21:17127000-17132000	Weak transcription	Fetal Heart	heart
17	chr21:17127000-17133400	Weak transcription	Pancreas	Pancrea
18	chr21:17127000-17147400	Weak transcription	HSMMtube	muscle
19	chr21:17127000-17152800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:17127200-17132000	Weak transcription	Psoas Muscle	Psoas
21	chr21:17127200-17132400	Weak transcription	Spleen	Spleen
22	chr21:17127200-17139400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr21:17127200-17140800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr21:17127200-17153400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr21:17127400-17133800	Weak transcription	Fetal Lung	lung
26	chr21:17127400-17146200	Weak transcription	NHDF-Ad	bronchial
27	chr21:17127400-17147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr21:17127400-17153400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr21:17127600-17145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:17127800-17131800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr21:17127800-17139400	Weak transcription	Fetal Kidney	kidney
32	chr21:17127800-17141600	Weak transcription	HMEC	breast
33	chr21:17127800-17152800	Weak transcription	Fetal Intestine Large	intestine
34	chr21:17128000-17132000	Weak transcription	Stomach Mucosa	stomach
35	chr21:17128000-17132400	Weak transcription	Colon Smooth Muscle	Colon
36	chr21:17128000-17132800	Weak transcription	Adipose Nuclei	Adipose
37	chr21:17128000-17135200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr21:17128000-17139400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:17128200-17132400	Weak transcription	Liver	Liver
40	chr21:17128200-17132400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr21:17128200-17139600	Weak transcription	Brain Anterior Caudate	brain
42	chr21:17128400-17138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:17128600-17131800	Weak transcription	HepG2	liver
44	chr21:17128800-17132200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr21:17128800-17139400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr21:17128800-17139400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr21:17129400-17131800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr21:17129400-17131800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr21:17129400-17131800	Weak transcription	Gastric	stomach
50	chr21:17129400-17131800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links