Variant report

Variant	rs1415974
Chromosome Location	chr1:67005503-67005504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10889624	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10889625	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11208903	1.00[CEU][hapmap];0.94[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];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[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]
rs1415984	1.00[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	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1947083	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2121051	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2859914	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4142763	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4655494	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655616	0.85[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	1.00[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]
rs7540195	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]
rs7543607	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs967322	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs967325	0.95[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs984409	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs994396	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1415974	TCTEX1D1	cis	cerebellum	SCAN
rs1415974	SGIP1	cis	cerebellum	SCAN
rs1415974	KPNB1	trans	cerebellum	SCAN
rs1415974	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67000200-67006400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:67000400-67008000	Weak transcription	Lung	lung
3	chr1:67000400-67022000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:67000800-67029800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:67001000-67006200	Weak transcription	HepG2	liver
6	chr1:67001000-67008000	Weak transcription	Left Ventricle	heart
7	chr1:67001200-67022000	Weak transcription	Right Ventricle	heart
8	chr1:67001600-67011000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:67001800-67006000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:67002000-67005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:67002000-67010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:67002200-67006400	Weak transcription	Osteobl	bone
13	chr1:67002600-67006000	Weak transcription	HUVEC	blood vessel
14	chr1:67002600-67006400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:67002800-67008200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:67003000-67006200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:67003000-67012400	Enhancers	Brain Hippocampus Middle	brain
18	chr1:67003800-67008000	Enhancers	Brain Anterior Caudate	brain
19	chr1:67004200-67009200	Enhancers	Brain Cingulate Gyrus	brain
20	chr1:67004200-67009600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:67004200-67012200	Enhancers	NHDF-Ad	bronchial
22	chr1:67004200-67012400	Enhancers	Fetal Heart	heart
23	chr1:67004400-67006600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:67004800-67005600	Enhancers	Aorta	Aorta
25	chr1:67004800-67005600	Enhancers	HMEC	breast
26	chr1:67004800-67006000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:67004800-67006000	Weak transcription	Fetal Brain Male	brain
28	chr1:67004800-67006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:67004800-67006800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:67004800-67006800	Enhancers	NHEK	skin
31	chr1:67004800-67012400	Enhancers	Brain Substantia Nigra	brain
32	chr1:67005000-67005600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:67005000-67005600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:67005000-67005600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:67005000-67005600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:67005000-67007000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:67005000-67007200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:67005000-67007200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr1:67005000-67007400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:67005000-67008600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:67005200-67005600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:67005200-67006400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr1:67005200-67007000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:67005200-67007000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:67005200-67007200	Enhancers	NH-A	brain
46	chr1:67005400-67005600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:67005400-67005600	Flanking Active TSS	NHLF	lung
48	chr1:67005400-67005800	Enhancers	Fetal Brain Female	brain
49	chr1:67005400-67006800	Enhancers	Fetal Lung	lung
50	chr1:67005400-67007000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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