Variant report

Variant	rs6662262
Chromosome Location	chr1:179517163-179517164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494515	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10494516	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs10913815	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913816	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs11577538	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11581440	0.87[ASN][1000 genomes]
rs11586725	0.91[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs11808258	0.81[ASN][1000 genomes]
rs1410587	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1410588	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854337	0.88[ASN][1000 genomes]
rs2149399	0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2274626	0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs2296960	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3767841	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs3829795	0.91[CHB][hapmap]
rs4652405	0.87[ASN][1000 genomes]
rs4652412	0.81[ASN][1000 genomes]
rs6666456	0.81[CHB][hapmap]
rs7519700	0.87[ASN][1000 genomes]
rs7541890	0.91[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7541899	0.87[ASN][1000 genomes]
rs7551440	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7551610	0.81[ASN][1000 genomes]
rs913514	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs928017	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9286930	0.86[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522746	chr1:179501365-179518459	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv523253	chr1:179516072-179518459	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6662262	TDRD5	cis	Thyroid	GTEx
rs6662262	TDRD5	cis	Nerve Tibial	GTEx
rs6662262	TDRD5	cis	Adipose Subcutaneous	GTEx
rs6662262	TDRD5	cis	Artery Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179510600-179520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:179514000-179518200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:179515400-179517800	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:179515600-179521800	Enhancers	Placenta	Placenta
5	chr1:179516000-179517800	Weak transcription	Pancreas	Pancrea
6	chr1:179516800-179519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:179516800-179520200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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