Variant report

Variant	rs59417472
Chromosome Location	chr1:93848513-93848514
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	chr1:93810264..93812351-chr1:93846551..93849161,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DR1-3	chr1:93847979-93851186	NONHSAT004532

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs1000607	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10782957	0.81[ASN][1000 genomes]
rs1081522	0.81[ASN][1000 genomes]
rs10874772	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10874773	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10874777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874778	0.86[ASN][1000 genomes]
rs11164902	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164904	0.81[ASN][1000 genomes]
rs11164916	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11576494	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12044883	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12124771	0.82[ASN][1000 genomes]
rs12133576	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133907	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138486	0.86[ASN][1000 genomes]
rs12139633	0.80[ASN][1000 genomes]
rs12406245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12752223	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1426318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535699	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1535701	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1559828	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1593512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2031225	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2031226	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2114273	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2391254	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2391256	0.86[ASN][1000 genomes]
rs3767962	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767964	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4000699	0.84[ASN][1000 genomes]
rs4240966	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847240	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847406	0.81[ASN][1000 genomes]
rs4847408	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4847410	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4847412	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531358	0.80[EUR][1000 genomes]
rs531514	0.82[EUR][1000 genomes]
rs535760	0.87[EUR][1000 genomes]
rs555161	0.80[EUR][1000 genomes]
rs569414	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602204	0.87[EUR][1000 genomes]
rs637646	0.86[EUR][1000 genomes]
rs6541401	0.87[EUR][1000 genomes]
rs6541404	0.87[EUR][1000 genomes]
rs6658257	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6680022	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6680107	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6694508	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703310	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs682514	0.86[EUR][1000 genomes]
rs687394	0.86[EUR][1000 genomes]
rs693737	0.87[EUR][1000 genomes]
rs7417952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512911	0.86[EUR][1000 genomes]
rs7524964	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7525248	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7526112	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7537403	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7540025	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541304	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7547244	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7551485	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs771478	0.81[ASN][1000 genomes]
rs771481	0.81[ASN][1000 genomes]
rs797661	0.81[EUR][1000 genomes]
rs797666	0.87[EUR][1000 genomes]
rs797671	0.82[EUR][1000 genomes]
rs797672	0.84[EUR][1000 genomes]
rs797681	0.87[EUR][1000 genomes]
rs942196	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9432453	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9432459	0.82[ASN][1000 genomes]
rs9432465	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9432681	0.89[EUR][1000 genomes];0.82[ASN][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	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs59417472	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs59417472	RP4-717I23.3	cis	Thyroid	GTEx
rs59417472	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs59417472	DR1	cis	Adipose Subcutaneous	GTEx
rs59417472	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs59417472	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs59417472	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs59417472	DR1	cis	multi-tissue	Pritchard
rs59417472	RP4-717I23.3	cis	lung	GTEx
rs59417472	RP4-717I23.3	cis	Artery Tibial	GTEx
rs59417472	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs59417472	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs59417472	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs59417472	RP4-717I23.3	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93835800-93850400	Weak transcription	Dnd41	blood
2	chr1:93840200-93851400	Weak transcription	Left Ventricle	heart
3	chr1:93840600-93852400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:93847200-93852000	Weak transcription	Aorta	Aorta
5	chr1:93848200-93850400	Enhancers	Fetal Lung	lung
6	chr1:93848400-93850000	Weak transcription	HSMMtube	muscle

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