Variant report

Variant	rs34578707
Chromosome Location	chr21:40675167-40675168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40674900..40676993-chr21:40757962..40759771,2	MCF-7	breast:
2	chr21:40671195..40673748-chr21:40675125..40678603,4	K562	blood:
3	chr21:40663279..40665811-chr21:40674696..40676596,2	K562	blood:
4	chr21:40673370..40675883-chr21:40685458..40687060,2	K562	blood:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000255568	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1041440	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427502	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151994	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12710453	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047663	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047678	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13049280	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13339986	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1541102	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984022	0.85[EUR][1000 genomes]
rs2026265	0.85[EUR][1000 genomes]
rs2026267	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2150415	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2735306	0.81[AMR][1000 genomes]
rs2735309	0.81[AMR][1000 genomes]
rs2776307	0.81[AMR][1000 genomes]
rs2776308	0.81[AMR][1000 genomes]
rs2776309	0.81[AMR][1000 genomes]
rs28360661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836928	0.82[AMR][1000 genomes]
rs2836944	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836955	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836965	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836967	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836968	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836972	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836973	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836974	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836977	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989330	0.91[AMR][1000 genomes]
rs34035316	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34433511	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34672724	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34978594	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123057	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35560196	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3945	0.83[AMR][1000 genomes]
rs55740356	0.84[AMR][1000 genomes]
rs55836299	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56306759	0.88[EUR][1000 genomes]
rs6517526	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517538	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66465538	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004583	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277978	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7282624	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283516	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283569	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354783	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128102	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128620	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128827	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8128894	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129147	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8129303	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8129355	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8130984	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133146	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8134733	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941894	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34578707	PSMG1	cis	Artery Tibial	GTEx
rs34578707	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs34578707	HMGN1	cis	multi-tissue	Pritchard
rs34578707	PSMG1	cis	Muscle Skeletal	GTEx
rs34578707	PSMG1	cis	Esophagus Mucosa	GTEx
rs34578707	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
2	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
4	chr21:40655000-40676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40655400-40683200	Strong transcription	Dnd41	blood
7	chr21:40655800-40677400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr21:40655800-40677400	Strong transcription	Fetal Thymus	thymus
9	chr21:40656400-40675400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:40656400-40676600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr21:40656400-40676800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:40659600-40676800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr21:40659600-40676800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr21:40661800-40683400	Weak transcription	Stomach Mucosa	stomach
16	chr21:40662400-40675400	Strong transcription	Osteobl	bone
17	chr21:40663600-40683400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:40663800-40676600	Strong transcription	Left Ventricle	heart
19	chr21:40664000-40684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr21:40665000-40683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr21:40665200-40684400	Weak transcription	Colonic Mucosa	Colon
22	chr21:40666000-40682600	Weak transcription	NHLF	lung
23	chr21:40667000-40684000	Weak transcription	HSMMtube	muscle
24	chr21:40667000-40684200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr21:40669200-40684200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr21:40669400-40676600	Strong transcription	Fetal Intestine Large	intestine
27	chr21:40669400-40684000	Weak transcription	HUVEC	blood vessel
28	chr21:40669400-40684400	Weak transcription	Esophagus	oesophagus
29	chr21:40669800-40676400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr21:40669800-40679800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr21:40669800-40683800	Weak transcription	Brain Substantia Nigra	brain
32	chr21:40670400-40677200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr21:40670400-40677400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr21:40670400-40680600	Weak transcription	Brain Hippocampus Middle	brain
35	chr21:40670400-40683800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr21:40670600-40676600	Strong transcription	Thymus	Thymus
37	chr21:40670600-40683200	Weak transcription	NHDF-Ad	bronchial
38	chr21:40670800-40679600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr21:40670800-40679800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr21:40670800-40680000	Weak transcription	HepG2	liver
41	chr21:40671400-40683200	Weak transcription	HMEC	breast
42	chr21:40671600-40676600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr21:40671600-40676600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:40672000-40675400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr21:40672200-40675800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr21:40672200-40684000	Weak transcription	Aorta	Aorta
47	chr21:40672400-40675200	Weak transcription	Ovary	ovary
48	chr21:40672400-40675400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr21:40672400-40683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr21:40672400-40684000	Weak transcription	Small Intestine	intestine

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