Variant report

Variant	rs12124731
Chromosome Location	chr1:84955752-84955753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84954216..84956546-chr1:84965976..84968272,2	MCF-7	breast:
2	chr1:84942484..84947798-chr1:84954955..84960241,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117133	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11163971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163980	0.81[CHB][hapmap]
rs11163981	0.81[CHB][hapmap]
rs11163992	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1144276	0.81[CHB][hapmap]
rs11578494	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12071149	0.81[CHB][hapmap]
rs12123381	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124568	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128801	0.81[CHB][hapmap]
rs12136756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12137559	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12140555	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143652	0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12145405	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1246159	0.81[CHB][hapmap]
rs1395416	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1395417	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1506707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17109982	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17110030	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911159	0.81[CHB][hapmap]
rs2271620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292808	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659173	0.81[CHB][hapmap]
rs2794218	0.81[CHB][hapmap]
rs312395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs312397	0.81[CHB][hapmap]
rs3813605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813607	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922538	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4906995	0.81[CHB][hapmap]
rs4907076	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907077	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907078	0.81[CHB][hapmap]
rs56212819	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57245302	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57442052	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704211	0.81[CHB][hapmap]
rs74095416	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74095424	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74095432	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74095436	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513490	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535445	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536988	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925740	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12124731	SPATA1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:84946000-84956400	Weak transcription	Gastric	stomach
3	chr1:84946000-84956400	Weak transcription	Spleen	Spleen
4	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
7	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:84946200-84956200	Weak transcription	Colonic Mucosa	Colon
10	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
11	chr1:84946400-84956200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:84946400-84956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:84946400-84962000	Weak transcription	Fetal Brain Male	brain
14	chr1:84946400-84962800	Weak transcription	Stomach Mucosa	stomach
15	chr1:84946600-84956400	Weak transcription	Psoas Muscle	Psoas
16	chr1:84946800-84967400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:84947000-84965800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:84947200-84956400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:84947200-84956400	Weak transcription	NHLF	lung
20	chr1:84947200-84958400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:84947400-84955800	Weak transcription	HMEC	breast
22	chr1:84947400-84957200	Weak transcription	Fetal Heart	heart
23	chr1:84947400-84957600	Weak transcription	Lung	lung
24	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
25	chr1:84947800-84966000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:84947800-84967800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:84948200-84956400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:84949600-84968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:84949800-84962000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:84951200-84956200	Weak transcription	Fetal Stomach	stomach
31	chr1:84951200-84956400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:84951400-84956400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:84951400-84956400	Weak transcription	Left Ventricle	heart
35	chr1:84951800-84956200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:84952400-84967400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:84953800-84968400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:84954000-84965800	Strong transcription	Dnd41	blood
39	chr1:84954400-84958600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:84954400-84963200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:84954800-84958000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:84954800-84959200	Strong transcription	NHEK	skin
43	chr1:84954800-84963400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:84954800-84965800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:84954800-84966400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:84954800-84966800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:84954800-84967000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:84954800-84967600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:84954800-84969200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:84955000-84957000	Strong transcription	K562	blood

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