Variant report

Variant	rs10490988
Chromosome Location	chr10:117702645-117702646
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10490986	0.94[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10490987	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10787611	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs10787612	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs1476795	1.00[CHD][hapmap]
rs1541466	1.00[CHD][hapmap]
rs1547947	1.00[CHD][hapmap]
rs17093700	1.00[CHD][hapmap]
rs17093786	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs17094083	1.00[ASW][hapmap]
rs17269525	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs17269882	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17269917	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17270580	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17270699	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17354680	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs17354968	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2024179	1.00[CHD][hapmap]
rs2054533	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2249295	0.89[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs2263622	0.86[EUR][1000 genomes]
rs2615874	0.84[CEU][hapmap];0.87[CHD][hapmap]
rs2615880	0.88[EUR][1000 genomes]
rs2615882	0.89[EUR][1000 genomes]
rs2615884	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.87[EUR][1000 genomes]
rs2615889	0.82[CEU][hapmap]
rs2620959	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620960	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2620961	0.94[CEU][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs2860341	1.00[CHD][hapmap]
rs2901061	1.00[CHD][hapmap]
rs2901094	0.84[CEU][hapmap];1.00[CHD][hapmap]
rs2960641	1.00[CHD][hapmap]
rs2960674	1.00[CHD][hapmap]
rs2960686	1.00[CHD][hapmap]
rs2960689	1.00[CHD][hapmap]
rs3781514	1.00[ASW][hapmap]
rs41284364	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55782493	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55917752	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56045626	0.98[EUR][1000 genomes]
rs57211763	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58744761	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61319078	0.90[EUR][1000 genomes]
rs67778998	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67945700	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7100412	0.84[CEU][hapmap]
rs72832833	0.84[EUR][1000 genomes]
rs72832834	0.88[EUR][1000 genomes]
rs72832836	0.89[EUR][1000 genomes]
rs73365760	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8416	1.00[ASW][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10490988	PDZD8	cis	cerebellum	SCAN
rs10490988	NANOS1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:117693800-117708600	Weak transcription	Fetal Muscle Leg	muscle
2	chr10:117697200-117704000	Weak transcription	A549	lung
3	chr10:117697600-117704800	Weak transcription	HSMM	muscle
4	chr10:117697600-117705200	Weak transcription	NH-A	brain
5	chr10:117700400-117702800	Enhancers	Fetal Lung	lung
6	chr10:117701000-117703800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:117701200-117704000	Weak transcription	NHEK	skin
8	chr10:117701400-117705200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:117701600-117705200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:117701600-117705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:117701800-117703000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr10:117701800-117704800	Weak transcription	HSMMtube	muscle
13	chr10:117702200-117704000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr10:117702200-117704800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:117702200-117705000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:117702200-117709000	Weak transcription	Ovary	ovary
17	chr10:117702400-117702800	Weak transcription	Fetal Kidney	kidney
18	chr10:117702400-117704200	Weak transcription	Fetal Heart	heart
19	chr10:117702400-117704800	Weak transcription	Osteobl	bone
20	chr10:117702400-117705200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:117702400-117705400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:117702400-117706600	Weak transcription	HUVEC	blood vessel
23	chr10:117702600-117702800	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:117702600-117704800	Weak transcription	NHDF-Ad	bronchial
25	chr10:117702600-117704800	Weak transcription	NHLF	lung

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