Variant report

Variant	rs2410106
Chromosome Location	chr21:40588950-40588951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40554637..40556936-chr21:40588612..40590641,2	K562	blood:
2	21:40583765-40590917..21:40718004-40719183	GM12878	blood:
3	21:40583765-40590917..21:40796857-40798340	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000183527	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000272991	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1065242	0.84[AMR][1000 genomes]
rs13048178	0.80[AMR][1000 genomes]
rs1984022	0.83[AMR][1000 genomes]
rs2026265	0.84[AMR][1000 genomes]
rs2234543	0.86[AMR][1000 genomes]
rs2836933	0.83[AMR][1000 genomes]
rs2836938	0.83[AMR][1000 genomes]
rs2836944	0.83[AMR][1000 genomes]
rs34035316	0.82[AMR][1000 genomes]
rs34978594	0.86[AMR][1000 genomes]
rs35386515	0.80[AMR][1000 genomes]
rs35571600	0.86[AMR][1000 genomes]
rs56306759	0.80[AMR][1000 genomes]
rs6517526	0.86[AMR][1000 genomes]
rs6517527	0.86[AMR][1000 genomes]
rs68090597	0.82[AMR][1000 genomes]
rs73221193	0.82[AMR][1000 genomes]
rs8128026	0.80[AMR][1000 genomes]
rs8128734	0.86[AMR][1000 genomes]
rs8129355	0.87[AMR][1000 genomes]
rs8131965	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS 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	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv3337818	chr21:40588653-40589057	Strong transcription Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2410106	PSMG1	cis	Artery Tibial	GTEx
rs2410106	PSMG1	cis	Esophagus Mucosa	GTEx
rs2410106	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2410106	PSMG1	cis	Muscle Skeletal	GTEx
rs2410106	PSMG1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr21:40565400-40653600	Strong transcription	Dnd41	blood
14	chr21:40565600-40590200	Strong transcription	Liver	Liver
15	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
17	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
20	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:40570600-40589800	Weak transcription	Stomach Mucosa	stomach
24	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
25	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
26	chr21:40573800-40593600	Weak transcription	A549	lung
27	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
28	chr21:40575200-40589400	Weak transcription	NHEK	skin
29	chr21:40576200-40590400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr21:40576400-40592400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr21:40576600-40589000	Strong transcription	Primary B cells from cord blood	blood
33	chr21:40576800-40589600	Weak transcription	HUVEC	blood vessel
34	chr21:40576800-40593600	Weak transcription	Right Atrium	heart
35	chr21:40577200-40593800	Weak transcription	Colon Smooth Muscle	Colon
36	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
37	chr21:40577600-40589400	Weak transcription	Brain Hippocampus Middle	brain
38	chr21:40577600-40596000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr21:40578000-40589000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr21:40578000-40589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr21:40578000-40595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr21:40578000-40598800	Weak transcription	Gastric	stomach
44	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
45	chr21:40578400-40589400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr21:40578600-40595400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40578600-40595400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
50	chr21:40579000-40598800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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