Variant report

Variant	rs1498354
Chromosome Location	chr1:67180489-67180490
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1014778	0.84[CEU][hapmap]
rs10789216	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889647	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10889649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208934	0.84[CEU][hapmap]
rs11208939	0.84[CEU][hapmap]
rs11208948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208951	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160675	0.81[CEU][hapmap]
rs11811067	0.82[ASN][1000 genomes]
rs11811699	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12063436	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12119578	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12128857	0.84[CEU][hapmap]
rs12138266	0.88[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1325268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1408852	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1445572	0.81[CEU][hapmap]
rs1547644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1838652	0.80[CEU][hapmap]
rs2016093	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs2181625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274987	0.86[AMR][1000 genomes]
rs2312573	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143026	0.84[CEU][hapmap]
rs473470	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs485122	0.85[ASN][1000 genomes]
rs487833	0.81[ASN][1000 genomes]
rs489300	0.98[ASN][1000 genomes]
rs512691	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs524204	0.80[ASN][1000 genomes]
rs538659	0.81[ASN][1000 genomes]
rs553729	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs562348	0.83[ASN][1000 genomes]
rs609939	0.81[ASN][1000 genomes]
rs624277	0.80[ASN][1000 genomes]
rs650202	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6588216	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6656461	0.84[CEU][hapmap]
rs6656705	0.84[CEU][hapmap]
rs6659325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6663604	0.87[AMR][1000 genomes]
rs6666600	0.84[CEU][hapmap]
rs6679379	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs682896	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs693956	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7512401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524680	0.84[CEU][hapmap]
rs7528346	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541249	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs9659684	0.84[CEU][hapmap]
rs9660797	0.84[CEU][hapmap]
rs9988481	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[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
rs1498354	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
2	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
7	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:67165200-67191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:67165400-67187600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:67165400-67191600	Weak transcription	Aorta	Aorta
12	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
13	chr1:67168000-67185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:67170200-67186800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:67171400-67189400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:67171400-67198000	Weak transcription	NHLF	lung
17	chr1:67177600-67189400	Weak transcription	Brain Anterior Caudate	brain
18	chr1:67177600-67189400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:67179600-67185000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:67179600-67191400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links