Variant report

Variant	rs6686064
Chromosome Location	chr1:150871297-150871298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10305720	0.81[EUR][1000 genomes]
rs10399947	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888394	0.80[EUR][1000 genomes]
rs10888395	0.82[EUR][1000 genomes]
rs10888397	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888398	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204726	0.80[EUR][1000 genomes]
rs11204739	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204742	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204743	0.88[ASN][1000 genomes]
rs11204747	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204748	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204749	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204750	0.87[ASN][1000 genomes]
rs11581757	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11589886	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11800855	0.86[EUR][1000 genomes]
rs12059949	0.87[ASN][1000 genomes]
rs12075597	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12085336	0.85[EUR][1000 genomes]
rs12090215	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12096831	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12097963	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409208	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12410394	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12410869	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1546376	0.87[ASN][1000 genomes]
rs16827671	0.80[EUR][1000 genomes]
rs1889740	0.86[EUR][1000 genomes]
rs1889741	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972060	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2004903	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2124952	0.90[ASN][1000 genomes]
rs2228099	0.86[EUR][1000 genomes]
rs2256355	0.86[EUR][1000 genomes]
rs2271076	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272214	0.88[ASN][1000 genomes]
rs2280627	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864873	0.86[EUR][1000 genomes]
rs2864882	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867296	0.83[ASN][1000 genomes]
rs2867297	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34985895	0.86[ASN][1000 genomes]
rs36008098	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3768013	0.85[EUR][1000 genomes]
rs3843843	0.90[ASN][1000 genomes]
rs3849279	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4451553	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970928	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970929	0.90[ASN][1000 genomes]
rs4970930	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970931	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970980	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4970982	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970984	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4970985	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4970986	0.90[ASN][1000 genomes]
rs59024312	0.90[ASN][1000 genomes]
rs59337856	0.80[EUR][1000 genomes]
rs6587542	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6658066	0.88[ASN][1000 genomes]
rs6660084	0.80[EUR][1000 genomes]
rs6660845	0.81[EUR][1000 genomes]
rs6669855	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66847267	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72704656	0.86[EUR][1000 genomes]
rs72704679	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704682	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704685	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7514004	0.86[EUR][1000 genomes]
rs7518156	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs752376	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528773	0.90[ASN][1000 genomes]
rs7532045	0.85[EUR][1000 genomes]
rs7556451	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556661	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8444	0.87[ASN][1000 genomes]
rs897815	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9661876	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs6686064	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6686064	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6686064	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs6686064	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6686064	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs6686064	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs6686064	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6686064	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6686064	RP11-316M1.12	cis	Thyroid	GTEx
rs6686064	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6686064	HORMAD1	cis	Nerve Tibial	GTEx
rs6686064	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6686064	RP11-316M1.12	cis	lung	GTEx
rs6686064	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6686064	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs6686064	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6686064	GOLPH3L	cis	Nerve Tibial	GTEx
rs6686064	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6686064	RP11-316M1.12	cis	Artery Tibial	GTEx
rs6686064	RP11-316M1.12	cis	Artery Aorta	GTEx
rs6686064	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6686064	RP11-316M1.12	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150868600-150874000	Weak transcription	Placenta	Placenta

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