Variant report

Variant	rs1445573
Chromosome Location	chr1:67047442-67047443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10127489	0.86[AFR][1000 genomes]
rs10127496	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10127497	0.86[AFR][1000 genomes]
rs10127994	0.86[AFR][1000 genomes]
rs10128053	0.94[ASW][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs10789212	0.90[JPT][hapmap]
rs10889636	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10889637	0.86[ASN][1000 genomes]
rs10889640	0.90[JPT][hapmap]
rs11208911	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs11208912	0.86[AFR][1000 genomes]
rs11208913	0.86[AFR][1000 genomes]
rs11208914	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11208927	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12023176	0.85[CHD][hapmap]
rs12027701	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12039282	0.85[CHD][hapmap]
rs12057164	0.84[AFR][1000 genomes]
rs12066541	0.86[AFR][1000 genomes]
rs12069946	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12070270	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12072937	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12074963	0.94[ASW][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs12085282	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12091471	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12091475	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1348674	0.86[AFR][1000 genomes]
rs1530490	0.84[AFR][1000 genomes]
rs1530491	0.94[ASW][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1867631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs2121042	0.84[AFR][1000 genomes]
rs2166307	0.87[ASW][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2166308	0.84[AFR][1000 genomes]
rs41405244	0.94[ASW][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs41418445	0.94[ASW][hapmap];0.96[YRI][hapmap]
rs41511845	0.94[ASW][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4655630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58171402	0.85[AFR][1000 genomes]
rs58274265	0.82[AFR][1000 genomes]
rs66552897	0.84[AFR][1000 genomes]
rs6665859	0.82[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6689138	0.84[AFR][1000 genomes]
rs6689333	0.84[AFR][1000 genomes]
rs6696366	0.84[AFR][1000 genomes]
rs67915022	0.84[AFR][1000 genomes]
rs7515444	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs7520226	0.90[ASN][1000 genomes]
rs7520353	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7532442	0.86[AFR][1000 genomes]
rs7536188	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7546090	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013351	chr1:67039730-67055937	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1003016	chr1:67043120-67067119	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1013476	chr1:67044630-67065911	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1445573	TCTEX1D1	cis	parietal	SCAN
rs1445573	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67041600-67062400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:67043200-67047600	Weak transcription	Fetal Lung	lung
3	chr1:67043200-67052000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:67043200-67056800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:67043200-67064400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:67043400-67056200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:67043600-67050600	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:67043600-67066600	Weak transcription	Fetal Brain Male	brain
9	chr1:67044000-67057200	Weak transcription	Aorta	Aorta
10	chr1:67044200-67064000	Weak transcription	NH-A	brain
11	chr1:67044800-67050600	Weak transcription	NHDF-Ad	bronchial
12	chr1:67044800-67064000	Weak transcription	Osteobl	bone
13	chr1:67045000-67047600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:67045000-67050400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:67045000-67050600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:67045000-67050600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:67045600-67056000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:67046000-67049400	Weak transcription	Psoas Muscle	Psoas
19	chr1:67046400-67060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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