Variant report

Variant	rs16824564
Chromosome Location	chr1:185812336-185812337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10911781	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1124757	0.90[EUR][1000 genomes]
rs11581777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11583867	0.95[CEU][hapmap];1.00[CHD][hapmap]
rs11807146	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[EUR][1000 genomes]
rs12057982	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063964	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12078015	0.90[EUR][1000 genomes]
rs12078444	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12079064	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12087032	0.95[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12098116	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1321668	0.82[EUR][1000 genomes]
rs1321669	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1321670	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1322359	0.95[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1322362	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1322364	0.82[EUR][1000 genomes]
rs13374445	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13376668	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407429	0.95[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1407430	0.95[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407431	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16824516	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16824576	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs17446906	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17447869	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448202	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17448216	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17448230	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17461534	0.83[CHD][hapmap]
rs17505819	0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17507044	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507170	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951517	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057381	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2057382	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2057383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2057384	0.97[EUR][1000 genomes]
rs2057385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2129125	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170859	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2220128	0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs35314812	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35425624	0.82[CEU][hapmap];0.85[CHD][hapmap];0.94[MEX][hapmap]
rs41357745	0.82[CEU][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs41458549	1.00[CHD][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4515745	0.82[EUR][1000 genomes]
rs4593772	0.82[EUR][1000 genomes]
rs4651287	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs4651288	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57398679	0.81[EUR][1000 genomes]
rs57686227	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61829860	0.91[EUR][1000 genomes]
rs61829884	0.81[EUR][1000 genomes]
rs6660510	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6692479	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7414598	0.82[EUR][1000 genomes]
rs7544533	0.95[CEU][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs900775	0.85[CHD][hapmap]
rs9628625	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][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	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16824564	NMNAT2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185803200-185850000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:185805600-185818200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:185807400-185812400	Weak transcription	HUVEC	blood vessel
4	chr1:185807400-185812600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:185811800-185813800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:185811800-185813800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:185812000-185813600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:185812000-185813600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:185812000-185813800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:185812000-185813800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:185812200-185812800	Weak transcription	Aorta	Aorta
12	chr1:185812200-185813000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:185812200-185813600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:185812200-185813800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links