Variant report

Variant	rs3922538
Chromosome Location	chr1:84959001-84959002
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84955760..84959867-chr1:84969764..84972842,4	MCF-7	breast:
2	chr1:84942484..84947798-chr1:84954955..84960241,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117133	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000174021	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11163971	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163972	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163992	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1123981	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578494	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11586006	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12123381	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12124568	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12124731	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12126584	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126924	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136756	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12137559	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12140555	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12143652	0.86[ASN][1000 genomes]
rs12145405	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395416	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1395417	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506707	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17109982	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17110030	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17110519	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292808	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs312395	0.94[ASN][1000 genomes]
rs3813605	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907076	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907077	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56212819	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57245302	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57442052	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74095416	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74095424	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74095432	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74095436	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512922	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513490	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514763	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7519606	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535445	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7536988	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs925740	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3922538	SPATA1	cis	putamen	BrainEAC
rs3922538	SPATA1	cis	intralobular white matter	BrainEAC
rs3922538	SPATA1	cis	brain	BrainEAC
rs3922538	SPATA1	cis	inferior olivary nucleus	BrainEAC
rs3922538	SPATA1	cis	frontal cortex	BrainEAC
rs3922538	SPATA1	cis	occipital cortex	BrainEAC
rs3922538	SPATA1	cis	temporal cortex	BrainEAC
rs3922538	SPATA1	cis	substantia nigra	BrainEAC
rs3922538	SPATA1	cis	hippocampus	BrainEAC
rs3922538	SPATA1	cis	thalamus	BrainEAC

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
4	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
7	chr1:84946400-84962000	Weak transcription	Fetal Brain Male	brain
8	chr1:84946400-84962800	Weak transcription	Stomach Mucosa	stomach
9	chr1:84946800-84967400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:84947000-84965800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
12	chr1:84947800-84966000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:84947800-84967800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:84949600-84968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:84949800-84962000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:84952400-84967400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:84953800-84968400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:84954000-84965800	Strong transcription	Dnd41	blood
20	chr1:84954400-84963200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:84954800-84959200	Strong transcription	NHEK	skin
22	chr1:84954800-84963400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:84954800-84965800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:84954800-84966400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:84954800-84966800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:84954800-84967000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:84954800-84967600	Strong transcription	Primary hematopoietic stem cells	blood
28	chr1:84954800-84969200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:84955000-84959400	Strong transcription	Placenta	Placenta
30	chr1:84955000-84960000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:84955000-84960000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:84955000-84960000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr1:84955000-84960200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:84955000-84960400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:84955000-84963400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:84955000-84963400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:84955000-84963600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:84955000-84963800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:84955000-84964200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:84955000-84964800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:84955000-84965600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:84955000-84965800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:84955000-84965800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:84955000-84966600	Strong transcription	Fetal Intestine Large	intestine
45	chr1:84955000-84966800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:84955000-84967000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:84955000-84967200	Strong transcription	Fetal Thymus	thymus
48	chr1:84955000-84967200	Strong transcription	HSMM	muscle
49	chr1:84955000-84967400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:84955000-84967400	Strong transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links