Variant report

Variant	rs1280309
Chromosome Location	chr1:67217254-67217255
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11208944	0.86[CEU][hapmap]
rs11208945	0.86[CEU][hapmap]
rs11811067	0.88[ASN][1000 genomes]
rs12119578	0.87[ASN][1000 genomes]
rs12138266	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12402709	0.87[CEU][hapmap]
rs1408852	0.82[CEU][hapmap]
rs2016093	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2274987	0.95[ASN][1000 genomes]
rs473470	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs485122	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487833	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs500905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512691	0.95[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs523544	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524204	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs531386	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538659	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs553729	0.91[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs562348	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs609906	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609939	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs610295	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624277	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs630410	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650202	0.82[CEU][hapmap]
rs657808	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6663604	0.97[ASN][1000 genomes]
rs6679379	0.83[ASN][1000 genomes]
rs678253	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs693956	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541249	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9988481	0.86[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1280309	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:67205400-67217600	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:67205600-67217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:67205800-67217400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:67205800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:67205800-67217800	Weak transcription	Aorta	Aorta
9	chr1:67207400-67217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:67207400-67217400	Weak transcription	Brain Anterior Caudate	brain
11	chr1:67212800-67217600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:67213200-67217600	Enhancers	HUVEC	blood vessel
13	chr1:67213600-67217600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:67213800-67217600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:67213800-67217600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:67215400-67217400	Enhancers	Primary T cells from cord blood	blood
17	chr1:67215600-67217600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:67215800-67217600	Weak transcription	NHDF-Ad	bronchial
19	chr1:67216000-67217400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:67216000-67217600	Weak transcription	Osteobl	bone
21	chr1:67216400-67217400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:67217000-67217400	Bivalent Enhancer	Primary B cells from cord blood	blood
23	chr1:67217000-67217400	Flanking Active TSS	Liver	Liver
24	chr1:67217200-67217400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
25	chr1:67217200-67217400	Enhancers	Brain Germinal Matrix	brain
26	chr1:67217200-67217600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:67217200-67217600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:67217200-67217600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:67217200-67217600	Enhancers	Placenta	Placenta
30	chr1:67217200-67217600	Weak transcription	NHLF	lung
31	chr1:67217200-67217800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:67217200-67217800	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr1:67217200-67217800	Bivalent Enhancer	Fetal Thymus	thymus
34	chr1:67217200-67217800	Enhancers	Left Ventricle	heart
35	chr1:67217200-67218000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
36	chr1:67217200-67218000	Enhancers	Lung	lung
37	chr1:67217200-67218400	Active TSS	Brain Angular Gyrus	brain
38	chr1:67217200-67218600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:67217200-67218800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr1:67217200-67219000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr1:67217200-67219200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr1:67217200-67220400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:67217200-67220800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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