Variant report

Variant	rs7540195
Chromosome Location	chr1:67002406-67002407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10889624	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10889625	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11208903	0.82[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143964	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1338184	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1338194	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1338200	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1415974	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1415984	0.81[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1547737	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1856315	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1947083	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2121051	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2859914	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4142763	0.81[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4655494	0.81[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655616	0.89[MKK][hapmap]
rs6588203	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6588204	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6691033	0.80[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7354930	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7354983	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7355221	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7543607	0.97[EUR][1000 genomes]
rs967322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs967325	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs984409	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs994396	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7540195	TCTEX1D1	cis	cerebellum	SCAN
rs7540195	SGIP1	cis	cerebellum	SCAN
rs7540195	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:66998400-67003200	Active TSS	Aorta	Aorta
2	chr1:66998800-67002600	Active TSS	NHDF-Ad	bronchial
3	chr1:66998800-67002800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:66998800-67003400	Active TSS	NHLF	lung
5	chr1:66999000-67002600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:66999000-67003600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:67000000-67004800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:67000000-67005000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:67000000-67005400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:67000200-67006400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:67000400-67003000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:67000400-67005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:67000400-67005200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:67000400-67008000	Weak transcription	Lung	lung
15	chr1:67000400-67022000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:67000800-67029800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:67001000-67002600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:67001000-67006200	Weak transcription	HepG2	liver
19	chr1:67001000-67008000	Weak transcription	Left Ventricle	heart
20	chr1:67001200-67002800	Active TSS	NH-A	brain
21	chr1:67001200-67022000	Weak transcription	Right Ventricle	heart
22	chr1:67001400-67003000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:67001400-67005400	Weak transcription	Fetal Lung	lung
24	chr1:67001600-67002600	Enhancers	Liver	Liver
25	chr1:67001600-67002600	Flanking Active TSS	Fetal Heart	heart
26	chr1:67001600-67011000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:67001800-67002600	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr1:67001800-67002800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr1:67001800-67003400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:67001800-67006000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:67002000-67002800	Enhancers	Brain Substantia Nigra	brain
32	chr1:67002000-67002800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:67002000-67003000	Active TSS	Brain Germinal Matrix	brain
34	chr1:67002000-67005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:67002000-67010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:67002200-67002600	Active TSS	Brain Anterior Caudate	brain
37	chr1:67002200-67002600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:67002200-67002600	Enhancers	HUVEC	blood vessel
39	chr1:67002200-67002800	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr1:67002200-67003000	Flanking Active TSS	Fetal Brain Male	brain
41	chr1:67002200-67006400	Weak transcription	Osteobl	bone
42	chr1:67002400-67002600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:67002400-67002600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:67002400-67002600	Enhancers	Stomach Mucosa	stomach
45	chr1:67002400-67003200	Active TSS	Fetal Brain Female	brain
46	chr1:67002400-67004200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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