Variant report

Variant	rs1988415
Chromosome Location	chr1:67024879-67024880
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	chr1:67008052..67009564-chr1:67023947..67025718,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10127489	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127497	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127994	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128053	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10159265	0.83[EUR][1000 genomes]
rs11208911	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11208912	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11208913	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12057164	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12066541	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12069946	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12070270	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12072937	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12074963	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12085282	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12091471	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12091475	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13376692	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs1348674	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1445574	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1530490	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1530491	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17129100	0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17129101	1.00[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17129226	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs17129244	0.94[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs17129245	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs17129252	0.94[CEU][hapmap]
rs17129269	0.94[CEU][hapmap]
rs17129307	0.94[CEU][hapmap]
rs17440390	0.94[CEU][hapmap]
rs1832417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20354	0.94[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2121042	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2166307	1.00[CEU][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2166308	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2182110	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs3901541	0.94[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41405244	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41418445	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs41511845	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55817355	0.83[EUR][1000 genomes]
rs55895340	0.80[EUR][1000 genomes]
rs57572851	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58064608	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58171402	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58274265	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58418199	0.83[EUR][1000 genomes]
rs61313508	0.83[EUR][1000 genomes]
rs6588210	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6588211	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6588212	0.94[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6588213	0.94[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs66552897	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6664698	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6689138	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6689183	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6689333	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6690186	0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs6696366	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67915022	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72669451	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72669463	0.80[EUR][1000 genomes]
rs72669465	0.80[EUR][1000 genomes]
rs72670251	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72676189	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72676194	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72676196	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72676198	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72679015	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74087510	0.83[EUR][1000 genomes]
rs7520353	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7528240	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7531750	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7532442	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7536634	0.94[CEU][hapmap]
rs7538967	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7540244	0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs7543378	0.94[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7545674	0.94[CEU][hapmap];0.87[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs920986	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.98[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	nsv1210	chr1:67017295-67033203	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1988415	TCTEX1D1	cis	parietal	SCAN
rs1988415	SGIP1	cis	parietal	SCAN
rs1988415	TCTEX1D1	cis	cerebellum	SCAN
rs1988415	ANGPTL3	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67000800-67029800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:67009800-67028200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:67010000-67029000	Weak transcription	Fetal Kidney	kidney
4	chr1:67011000-67028000	Weak transcription	HUVEC	blood vessel
5	chr1:67011800-67029800	Weak transcription	Fetal Brain Male	brain
6	chr1:67019000-67028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:67020200-67028200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:67022200-67025000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:67022200-67027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:67022400-67027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:67022400-67028200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:67022400-67028200	Weak transcription	Left Ventricle	heart
13	chr1:67022400-67028200	Weak transcription	NH-A	brain
14	chr1:67022400-67028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:67022400-67028400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:67022600-67025200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:67023000-67028400	Weak transcription	NHEK	skin
18	chr1:67023200-67027600	Weak transcription	Osteobl	bone
19	chr1:67023400-67025200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:67023400-67027600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:67023400-67028000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:67023400-67028600	Weak transcription	Brain Anterior Caudate	brain
23	chr1:67023400-67028800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:67023600-67025000	Weak transcription	Fetal Lung	lung
25	chr1:67023600-67025400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:67023600-67028200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:67023800-67025000	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:67023800-67025400	Weak transcription	Brain Angular Gyrus	brain
29	chr1:67023800-67027400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:67023800-67028800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:67024000-67025000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:67024000-67025000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:67024000-67026400	Weak transcription	NHDF-Ad	bronchial
34	chr1:67024000-67028200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:67024600-67025600	Enhancers	Aorta	Aorta
36	chr1:67024800-67025000	Enhancers	NHLF	lung
37	chr1:67024800-67025400	Enhancers	Brain Substantia Nigra	brain
38	chr1:67024800-67026200	Enhancers	Fetal Heart	heart

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