Variant report

Variant	rs10854484
Chromosome Location	chr21:47926702-47926703
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	chr21:47920603..47923397-chr21:47924852..47927519,2	K562	blood:
2	chr21:47921897..47925643-chr21:47925841..47927519,3	K562	blood:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1008548	0.87[ASN][1000 genomes]
rs1008549	0.87[ASN][1000 genomes]
rs1029231	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11089070	0.83[ASN][1000 genomes]
rs11700596	0.86[ASN][1000 genomes]
rs11701310	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11701571	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11701815	0.88[ASN][1000 genomes]
rs11701902	0.85[ASN][1000 genomes]
rs11702190	0.84[ASN][1000 genomes]
rs11702278	0.88[ASN][1000 genomes]
rs11702701	0.87[ASN][1000 genomes]
rs11702704	0.84[ASN][1000 genomes]
rs11702822	0.84[ASN][1000 genomes]
rs12627084	0.88[ASN][1000 genomes]
rs1892691	0.88[ASN][1000 genomes]
rs1892692	0.88[ASN][1000 genomes]
rs2070432	0.92[ASN][1000 genomes]
rs2070433	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070435	0.92[ASN][1000 genomes]
rs2073380	0.83[ASN][1000 genomes]
rs2096507	0.87[ASN][1000 genomes]
rs2268524	0.83[ASN][1000 genomes]
rs2839269	0.87[ASN][1000 genomes]
rs2839277	0.81[ASN][1000 genomes]
rs2839278	0.81[ASN][1000 genomes]
rs2839279	0.81[ASN][1000 genomes]
rs2839281	0.83[ASN][1000 genomes]
rs2839288	0.83[ASN][1000 genomes]
rs2839290	0.81[ASN][1000 genomes]
rs2839295	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839301	0.84[ASN][1000 genomes]
rs2839302	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839304	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839306	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2839311	0.87[ASN][1000 genomes]
rs2839312	0.92[ASN][1000 genomes]
rs2839314	0.92[ASN][1000 genomes]
rs28613801	0.82[ASN][1000 genomes]
rs28702984	0.87[ASN][1000 genomes]
rs4276098	0.86[ASN][1000 genomes]
rs4347941	0.89[ASN][1000 genomes]
rs55744579	0.87[ASN][1000 genomes]
rs56016846	0.83[ASN][1000 genomes]
rs56134005	0.85[ASN][1000 genomes]
rs56157650	0.92[ASN][1000 genomes]
rs6518299	0.87[ASN][1000 genomes]
rs6518300	0.88[ASN][1000 genomes]
rs66799972	0.83[ASN][1000 genomes]
rs718496	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs721131	0.92[ASN][1000 genomes]
rs725970	0.88[ASN][1000 genomes]
rs7277986	0.87[ASN][1000 genomes]
rs7279002	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7282515	0.88[ASN][1000 genomes]
rs73152849	0.87[ASN][1000 genomes]
rs8127582	0.83[ASN][1000 genomes]
rs8129305	0.83[ASN][1000 genomes]
rs8129793	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8130209	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8132725	0.89[ASN][1000 genomes]
rs9306156	0.91[ASN][1000 genomes]
rs9306157	0.92[ASN][1000 genomes]
rs9637220	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9637225	0.91[ASN][1000 genomes]
rs9647244	0.83[ASN][1000 genomes]
rs9647245	0.83[ASN][1000 genomes]
rs9975875	0.84[ASN][1000 genomes]
rs9976530	0.81[ASN][1000 genomes]
rs9980470	0.88[ASN][1000 genomes]
rs9981212	0.88[ASN][1000 genomes]
rs9981387	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
2	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
3	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
4	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
5	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
6	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
7	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
10	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
11	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
12	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
14	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
15	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
16	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
18	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers 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 miRNA target site	56 gene(s)	inside rSNPs	n/a
19	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	30 gene(s)	inside rSNPs	n/a
20	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
23	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
26	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10854484	S100B	cis	Whole Blood	GTEx
rs10854484	DIP2A	cis	Whole Blood	GTEx
rs10854484	C21orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47880400-47931200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr21:47904200-47931200	Weak transcription	Psoas Muscle	Psoas
3	chr21:47909600-47932400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:47910400-47929000	Weak transcription	Fetal Heart	heart
5	chr21:47911400-47933600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr21:47912600-47926800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:47913000-47935000	Weak transcription	Right Atrium	heart
8	chr21:47913400-47931400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:47915200-47933400	Strong transcription	Fetal Stomach	stomach
10	chr21:47916800-47929200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:47918800-47929000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:47918800-47930000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr21:47918800-47932600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:47919000-47931200	Weak transcription	Fetal Brain Male	brain
15	chr21:47919400-47929600	Weak transcription	Esophagus	oesophagus
16	chr21:47919400-47933400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:47920200-47928600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr21:47920200-47930800	Weak transcription	Pancreas	Pancrea
19	chr21:47920400-47929000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr21:47920600-47929000	Weak transcription	Colonic Mucosa	Colon
21	chr21:47920600-47929800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr21:47920600-47935600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr21:47920800-47929000	Weak transcription	HSMMtube	muscle
24	chr21:47920800-47929600	Weak transcription	Brain Hippocampus Middle	brain
25	chr21:47920800-47931200	Weak transcription	Small Intestine	intestine
26	chr21:47921000-47928800	Weak transcription	HUVEC	blood vessel
27	chr21:47921000-47929000	Weak transcription	Stomach Mucosa	stomach
28	chr21:47921000-47929000	Weak transcription	K562	blood
29	chr21:47921200-47929200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr21:47921200-47929200	Weak transcription	A549	lung
31	chr21:47921400-47933400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr21:47921600-47928800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr21:47921600-47929200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr21:47921800-47927600	Strong transcription	Dnd41	blood
35	chr21:47921800-47931400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr21:47921800-47933000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr21:47922000-47928600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr21:47922000-47928800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr21:47922000-47929800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr21:47922200-47929000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:47922400-47926800	Strong transcription	Placenta	Placenta
42	chr21:47922600-47927000	Strong transcription	Primary T cells from cord blood	blood
43	chr21:47922600-47927000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr21:47922600-47927000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr21:47923000-47933000	Strong transcription	Fetal Intestine Large	intestine
46	chr21:47923600-47932000	Strong transcription	Fetal Intestine Small	intestine
47	chr21:47923800-47927000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:47924000-47927000	Strong transcription	Fetal Lung	lung
49	chr21:47924000-47927000	Strong transcription	NHEK	skin
50	chr21:47924000-47927200	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links