Variant report

Variant	rs7542924
Chromosome Location	chr1:67143055-67143056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:67142376-67143148	SK-N-SH	brain:	n/a	n/a
2	FOS	chr1:67142600-67143071	HUVEC	blood vessel:	n/a	chr1:67142813-67142823 chr1:67142813-67142822 chr1:67142813-67142823 chr1:67142813-67142823 chr1:67142812-67142823 chr1:67142981-67142990 chr1:67142813-67142823
3	MAFK	chr1:67142672-67143177	IMR90	lung:	n/a	chr1:67142867-67142883

Variant related genes	Relation type
ENSG00000248458	TF binding region
SGIP1	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1032634	0.95[CEU][hapmap]
rs1032635	0.96[CEU][hapmap]
rs10749763	0.96[CEU][hapmap]
rs10749765	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10789210	0.95[CEU][hapmap]
rs10789214	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10789215	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10889634	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs10889635	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs10889641	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10889642	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10889643	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10889644	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11208932	0.82[EUR][1000 genomes]
rs1280280	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1280310	0.88[CEU][hapmap]
rs1325261	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1325263	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1329978	0.82[EUR][1000 genomes]
rs1536115	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1562217	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs1570815	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1856318	0.84[CEU][hapmap]
rs2025595	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2031478	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2146904	0.96[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs2147777	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2483704	0.96[CEU][hapmap]
rs2483705	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2872078	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2916	0.88[CEU][hapmap]
rs4655506	1.00[CEU][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4655636	0.92[CEU][hapmap]
rs4655647	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs4655648	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4655650	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs485521	0.96[CEU][hapmap]
rs492109	0.87[EUR][1000 genomes]
rs499263	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs502690	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs523132	0.96[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs523188	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs523956	0.96[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs524114	0.96[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs536410	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs536527	0.96[CEU][hapmap]
rs539014	0.88[CEU][hapmap]
rs602513	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs603750	0.96[CEU][hapmap]
rs618093	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs628655	0.88[CEU][hapmap]
rs6588207	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs6588215	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs659291	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs665319	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6656550	0.85[EUR][1000 genomes]
rs6656912	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs6659968	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6668603	0.88[EUR][1000 genomes]
rs6669023	0.88[EUR][1000 genomes]
rs6670378	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6680876	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6680944	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6681460	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6689864	0.96[CEU][hapmap]
rs6696927	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs6697088	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs7519747	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7521111	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7521123	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7524818	0.96[CEU][hapmap]
rs7538938	0.84[EUR][1000 genomes]
rs7554101	0.96[CEU][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs9659879	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9662943	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9662962	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7542924	TCTEX1D1	cis	cerebellum	SCAN
rs7542924	TCTEX1D1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
2	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
3	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
4	chr1:67111400-67154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:67121200-67145400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:67135200-67154200	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:67135600-67155400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:67137400-67148000	Weak transcription	Fetal Brain Female	brain
10	chr1:67137600-67155000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:67137800-67155000	Weak transcription	Fetal Brain Male	brain
12	chr1:67138000-67147200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:67138000-67154800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:67139200-67146400	Weak transcription	Fetal Lung	lung
15	chr1:67139600-67148000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:67139800-67145400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:67140400-67154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
19	chr1:67140800-67147400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:67141200-67148800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:67141600-67144800	Enhancers	NH-A	brain
22	chr1:67141800-67143400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:67141800-67143600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:67141800-67144600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:67141800-67144600	Enhancers	HUVEC	blood vessel
26	chr1:67142000-67143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:67142000-67143400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:67142200-67143200	Enhancers	Adipose Nuclei	Adipose
29	chr1:67142200-67143400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:67142200-67143400	Enhancers	HSMM	muscle
31	chr1:67142200-67145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:67142400-67143400	Enhancers	Fetal Kidney	kidney
33	chr1:67142400-67144000	Enhancers	Osteobl	bone
34	chr1:67142400-67145200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:67142400-67148000	Weak transcription	Aorta	Aorta
36	chr1:67142600-67144600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:67142600-67144800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:67142600-67147200	Weak transcription	NHLF	lung
39	chr1:67142800-67147200	Weak transcription	NHDF-Ad	bronchial
40	chr1:67143000-67143400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:67143000-67143400	Flanking Active TSS	HSMMtube	muscle
42	chr1:67143000-67144800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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