Variant report

Variant	rs344092
Chromosome Location	chr3:156564320-156564321
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156557512..156559174-chr3:156562252..156564501,2	K562	blood:
2	chr3:156549286..156551711-chr3:156563760..156565541,2	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10936040	0.85[YRI][hapmap]
rs11710516	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11717138	1.00[JPT][hapmap]
rs11927500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634915	0.81[YRI][hapmap]
rs13321802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13322318	0.81[YRI][hapmap]
rs1355280	1.00[CHB][hapmap]
rs1430412	1.00[JPT][hapmap]
rs1510270	1.00[CHB][hapmap]
rs168248	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs16826858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16826899	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16826906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs171080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs180747	1.00[CHB][hapmap]
rs182936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs184677	1.00[CHB][hapmap]
rs193198	1.00[CHB][hapmap]
rs193423	1.00[CHB][hapmap]
rs2054881	1.00[CHB][hapmap]
rs2129909	1.00[CHB][hapmap]
rs2321290	0.85[YRI][hapmap]
rs237246	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2633815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653817	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2665390	1.00[CHB][hapmap]
rs28661978	0.95[ASN][1000 genomes]
rs2874490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2874491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs343992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344005	1.00[CHB][hapmap]
rs344006	1.00[CHB][hapmap]
rs344008	1.00[CHB][hapmap]
rs344009	1.00[CHB][hapmap]
rs344010	1.00[CHB][hapmap]
rs344011	1.00[CHB][hapmap]
rs344012	1.00[CHB][hapmap]
rs344013	1.00[CHB][hapmap]
rs344014	1.00[CHB][hapmap]
rs344015	1.00[CHB][hapmap]
rs344016	1.00[CHB][hapmap]
rs344017	1.00[CHB][hapmap]
rs344052	1.00[CHB][hapmap]
rs344053	1.00[CHB][hapmap]
rs344054	1.00[CHB][hapmap]
rs344055	1.00[CHB][hapmap]
rs344058	1.00[CHB][hapmap]
rs344059	1.00[CHB][hapmap]
rs344060	1.00[CHB][hapmap]
rs344061	1.00[CHB][hapmap]
rs344062	1.00[CHB][hapmap]
rs344063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344064	1.00[CHB][hapmap]
rs344065	1.00[CHB][hapmap]
rs344066	1.00[CHB][hapmap]
rs344068	1.00[CHB][hapmap]
rs344069	1.00[CHB][hapmap]
rs344070	1.00[CHB][hapmap]
rs344074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs344076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs344077	0.95[ASN][1000 genomes]
rs344078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs344081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs344085	0.95[ASN][1000 genomes]
rs344086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344088	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344089	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs344090	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344093	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3796172	1.00[JPT][hapmap]
rs414683	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419287	1.00[CHB][hapmap]
rs427384	1.00[CHB][hapmap]
rs4429586	1.00[CHB][hapmap]
rs4441614	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55850252	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58207863	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59244547	0.95[ASN][1000 genomes]
rs6441095	1.00[CHB][hapmap]
rs6441099	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441100	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441103	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763644	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6774702	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6786167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787952	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6792917	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6795327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6795516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6802042	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6802511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7426821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7609851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7618306	1.00[JPT][hapmap]
rs7621699	0.84[ASN][1000 genomes]
rs7630909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7640994	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7650127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs978108	1.00[CHB][hapmap]
rs9810194	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9823112	1.00[CHB][hapmap]
rs9841269	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9844054	0.81[YRI][hapmap]
rs9847692	1.00[JPT][hapmap]
rs9861359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871817	0.81[YRI][hapmap]
rs9876010	0.80[YRI][hapmap]
rs9878709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs344092	LEKR1	cis	Thyroid	GTEx
rs344092	LEKR1	cis	Heart Left Ventricle	GTEx
rs344092	LINC00886	cis	Artery Aorta	GTEx
rs344092	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156561800-156565200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:156561800-156565200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:156561800-156565200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:156561800-156565200	Weak transcription	NHDF-Ad	bronchial

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