Variant report

Variant	rs9977762
Chromosome Location	chr21:40627206-40627207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40617287..40619238-chr21:40626430..40628047,2	MCF-7	breast:
2	chr21:40625733..40628275-chr21:40724083..40725744,2	MCF-7	breast:
3	chr21:40626308..40628705-chr21:40634395..40637169,2	K562	blood:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1011413	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10154217	0.81[ASN][1000 genomes]
rs11911822	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12626405	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1882779	0.81[ASN][1000 genomes]
rs1888487	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836969	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836971	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836975	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836982	0.82[ASN][1000 genomes]
rs35909862	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4816620	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4818005	0.83[ASN][1000 genomes]
rs4818015	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6517535	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs719230	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7276774	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7278985	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7281853	0.81[ASN][1000 genomes]
rs997147	0.82[ASN][1000 genomes]
rs9974757	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9978775	0.82[ASN][1000 genomes]
rs9982111	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9977762	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs9977762	PSMG1	cis	Artery Tibial	GTEx
rs9977762	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs9977762	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs9977762	PSMG1	cis	Esophagus Mucosa	GTEx
rs9977762	PSMG1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:40565400-40653600	Strong transcription	Dnd41	blood
9	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
11	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
12	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr21:40597200-40635600	Weak transcription	Fetal Heart	heart
16	chr21:40598200-40629800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr21:40603000-40627800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
19	chr21:40608400-40628400	Weak transcription	Lung	lung
20	chr21:40608400-40632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr21:40608400-40632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr21:40608400-40634200	Weak transcription	NHLF	lung
23	chr21:40608400-40638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr21:40608600-40628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr21:40608600-40636400	Weak transcription	Aorta	Aorta
27	chr21:40609200-40627600	Weak transcription	Right Ventricle	heart
28	chr21:40609800-40635400	Weak transcription	Fetal Brain Male	brain
29	chr21:40612200-40628600	Weak transcription	Brain Anterior Caudate	brain
30	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr21:40613800-40651000	Strong transcription	Fetal Thymus	thymus
32	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr21:40614200-40628400	Strong transcription	Fetal Intestine Large	intestine
34	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr21:40614800-40635000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr21:40615800-40639800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr21:40616400-40630600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr21:40616400-40631000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr21:40616400-40651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr21:40616600-40631400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr21:40617200-40628400	Weak transcription	Pancreas	Pancrea
43	chr21:40617400-40635200	Weak transcription	Colonic Mucosa	Colon
44	chr21:40617600-40628600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr21:40618000-40632200	Weak transcription	NHEK	skin
46	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
47	chr21:40618400-40635400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr21:40619000-40628200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr21:40619000-40638000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:40619200-40627400	Weak transcription	Fetal Brain Female	brain

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