Variant report

Variant	rs16826858
Chromosome Location	chr3:156578398-156578399
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156573384..156575270-chr3:156577093..156579148,2	K562	blood:

Extended variants
information (count: 128 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10212230	0.81[YRI][hapmap]
rs10936040	0.85[YRI][hapmap]
rs11710516	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11717138	1.00[JPT][hapmap]
rs11927500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634915	0.81[YRI][hapmap]
rs13088978	0.81[YRI][hapmap]
rs13321802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13322318	0.81[YRI][hapmap]
rs1355280	1.00[CHB][hapmap]
rs1430412	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1510270	1.00[CHB][hapmap]
rs168248	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs16826864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16826899	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16826906	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.83[CHD][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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653817	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.80[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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2874491	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs343992	1.00[CHB][hapmap];1.00[CHD][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];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs344076	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[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];0.97[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[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs344085	0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[ASN][1000 genomes]
rs344086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344088	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344089	0.96[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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344092	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]
rs344093	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3796172	1.00[JPT][hapmap]
rs414683	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[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	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680298	0.83[CHD][hapmap]
rs4680299	0.83[CHD][hapmap]
rs491423	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55850252	0.97[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];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441100	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441103	0.89[ASW][hapmap];0.97[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[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	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6774702	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6786167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[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];0.95[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];0.81[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]
rs6799457	0.83[CHD][hapmap]
rs6802042	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6802511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7426821	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7609851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7616633	0.81[GIH][hapmap]
rs7618306	1.00[CHD][hapmap];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];1.00[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];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7640994	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7650127	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs978108	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9810194	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9823112	1.00[CHB][hapmap]
rs9841269	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9844054	0.81[YRI][hapmap]
rs9847187	0.81[YRI][hapmap]
rs9847692	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9861359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[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]
rs9878585	0.81[YRI][hapmap]
rs9878709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[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	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
2	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16826858	LEKR1	cis	Thyroid	GTEx
rs16826858	VEPH1	cis	cerebellum	SCAN
rs16826858	LINC00886	cis	Artery Aorta	GTEx
rs16826858	C3orf33	cis	parietal	SCAN
rs16826858	LEKR1	cis	cerebellum	SCAN
rs16826858	LEKR1	cis	Heart Left Ventricle	GTEx
rs16826858	LINC00886	cis	Artery Tibial	GTEx
rs16826858	SLC23A3	trans	parietal	SCAN
rs16826858	LEKR1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156577200-156578400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:156577600-156578400	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr3:156578200-156578600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:156578200-156579200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:156578200-156579400	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links