Variant report

Variant	rs473470
Chromosome Location	chr1:67205327-67205328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67203426..67206890-chr1:67208390..67210914,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10889647	0.81[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes]
rs10889649	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11208944	0.91[CEU][hapmap]
rs11208945	0.91[CEU][hapmap]
rs11208948	0.81[JPT][hapmap]
rs11208951	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11811067	0.98[ASN][1000 genomes]
rs12043460	0.84[AMR][1000 genomes]
rs12119578	0.97[ASN][1000 genomes]
rs12138266	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12402709	0.90[CEU][hapmap];0.84[AMR][1000 genomes]
rs1280309	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]
rs1315210	0.86[ASN][1000 genomes]
rs1325268	0.81[JPT][hapmap]
rs1408852	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs1498354	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1547644	0.80[ASN][1000 genomes]
rs16844	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2016093	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2181625	0.80[ASN][1000 genomes]
rs2274987	0.84[ASN][1000 genomes]
rs2647386	0.83[AMR][1000 genomes]
rs35886191	0.83[AMR][1000 genomes]
rs3738167	0.82[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs485122	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489300	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs492358	0.82[ASN][1000 genomes]
rs500905	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs510771	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs512691	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs523544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531386	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs538659	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs553729	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55771540	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56219542	0.83[ASN][1000 genomes]
rs562348	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609707	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs609906	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs609939	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610295	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs624277	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630410	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs650202	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs657808	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659325	0.81[JPT][hapmap]
rs6663604	0.87[ASN][1000 genomes]
rs6679379	0.94[ASN][1000 genomes]
rs678253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs678499	0.90[YRI][hapmap]
rs682896	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs693956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512401	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs7541249	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9988481	0.85[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs473470	TCTEX1D1	cis	multi-tissue	Pritchard
rs473470	TCTEX1D1	cis	Whole Blood	GTEx
rs473470	TCTEX1D1	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
3	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:67192200-67208200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:67196600-67212800	Weak transcription	Fetal Brain Female	brain
8	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:67199600-67205600	Weak transcription	NHLF	lung
10	chr1:67199600-67206400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:67203000-67206000	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:67203000-67208600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:67203400-67205400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:67203400-67206400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:67203600-67205400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:67203800-67208000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:67204000-67205800	Enhancers	NHDF-Ad	bronchial
18	chr1:67204000-67206600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:67204200-67206000	Strong transcription	Brain Anterior Caudate	brain
20	chr1:67204600-67205400	Strong transcription	Brain Hippocampus Middle	brain
21	chr1:67204600-67205600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:67204600-67205800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:67204600-67205800	Strong transcription	Aorta	Aorta
24	chr1:67204600-67205800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr1:67204800-67205400	ZNF genes & repeats	Lung	lung
26	chr1:67204800-67205600	Enhancers	Left Ventricle	heart
27	chr1:67204800-67205800	Enhancers	Fetal Thymus	thymus
28	chr1:67204800-67205800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr1:67205000-67205400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:67205000-67205600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:67205000-67205600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:67205000-67205600	Enhancers	Right Ventricle	heart
33	chr1:67205000-67205600	Enhancers	Osteobl	bone
34	chr1:67205000-67205800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:67205000-67205800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:67205000-67205800	Enhancers	Primary T cells from cord blood	blood
37	chr1:67205000-67205800	Enhancers	Fetal Heart	heart
38	chr1:67205000-67205800	Enhancers	Dnd41	blood
39	chr1:67205000-67205800	Enhancers	K562	blood
40	chr1:67205000-67206000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:67205200-67205600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:67205200-67205600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:67205200-67205600	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:67205200-67205600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr1:67205200-67205600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:67205200-67205600	Enhancers	Fetal Muscle Leg	muscle
47	chr1:67205200-67205800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:67205200-67205800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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