Variant report

Variant	rs11577538
Chromosome Location	chr1:179517714-179517715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10494515	0.82[CHB][hapmap]
rs10494516	0.82[CHB][hapmap]
rs10494517	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10494518	0.87[ASW][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];0.88[ASN][1000 genomes]
rs1079291	0.88[EUR][1000 genomes]
rs10913815	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10913816	0.82[CHB][hapmap]
rs11581470	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs11585517	0.82[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs11586725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808258	0.87[ASW][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];0.92[ASN][1000 genomes]
rs12566954	0.88[ASN][1000 genomes]
rs1410585	0.85[ASN][1000 genomes]
rs1410587	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1410588	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1410591	0.81[ASN][1000 genomes]
rs1410592	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs16854042	0.90[JPT][hapmap]
rs16854244	0.88[ASN][1000 genomes]
rs1999068	0.83[EUR][1000 genomes]
rs2149399	0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs2209922	0.87[ASW][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[MKK][hapmap];0.88[ASN][1000 genomes]
rs2274622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2274626	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[ASN][1000 genomes]
rs2296960	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3754132	0.89[ASN][1000 genomes]
rs3765547	0.89[CEU][hapmap];0.82[JPT][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap]
rs3767840	0.81[ASN][1000 genomes]
rs3767841	0.82[CHB][hapmap]
rs3829795	0.82[CHB][hapmap]
rs4072452	0.81[JPT][hapmap]
rs4111171	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs41267596	0.88[ASN][1000 genomes]
rs4651042	0.88[ASN][1000 genomes]
rs4652369	0.81[JPT][hapmap]
rs4652380	0.81[JPT][hapmap]
rs4652406	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4652407	0.88[ASN][1000 genomes]
rs4652408	0.88[ASN][1000 genomes]
rs4652412	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs55908143	0.88[ASN][1000 genomes]
rs56071531	0.88[ASN][1000 genomes]
rs57340322	0.86[ASN][1000 genomes]
rs6425557	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6425572	0.88[ASN][1000 genomes]
rs6425574	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6658180	0.88[ASN][1000 genomes]
rs6662262	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs6666456	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs6674086	0.87[ASW][hapmap];0.87[MKK][hapmap]
rs6679542	0.91[JPT][hapmap]
rs6700149	0.81[JPT][hapmap]
rs72704477	0.89[ASN][1000 genomes]
rs7413415	0.81[JPT][hapmap]
rs744446	0.84[EUR][1000 genomes]
rs7519700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529107	0.88[ASN][1000 genomes]
rs7541890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541899	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548654	0.87[ASN][1000 genomes]
rs7551440	0.81[CHD][hapmap]
rs7551610	0.92[ASN][1000 genomes]
rs913514	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs928017	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs9286930	0.95[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs964983	0.87[ASW][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.98[MKK][hapmap];0.88[ASN][1000 genomes]
rs964984	0.87[ASW][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];0.88[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11577538	TDRD5	cis	cerebellum	SCAN
rs11577538	TDRD5	cis	parietal	SCAN
rs11577538	TDRD5	cis	Artery Aorta	GTEx
rs11577538	TDRD5	cis	Artery Tibial	GTEx
rs11577538	TDRD5	cis	Adipose Subcutaneous	GTEx
rs11577538	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs11577538	SOAT1	cis	cerebellum	SCAN
rs11577538	TDRD5	cis	Esophagus Mucosa	GTEx
rs11577538	TDRD5	cis	Nerve Tibial	GTEx
rs11577538	TDRD5	cis	lung	GTEx
rs11577538	TDRD5	cis	Thyroid	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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