Variant report

Variant	rs12078444
Chromosome Location	chr1:185855289-185855290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10047250	1.00[JPT][hapmap]
rs10465500	1.00[JPT][hapmap]
rs10489714	1.00[JPT][hapmap]
rs10489715	1.00[JPT][hapmap]
rs10489716	1.00[JPT][hapmap]
rs10489717	1.00[JPT][hapmap]
rs10911781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911785	1.00[JPT][hapmap]
rs10911789	1.00[JPT][hapmap]
rs11581777	0.85[ASN][1000 genomes]
rs11583867	1.00[CHD][hapmap]
rs11586312	0.87[EUR][1000 genomes]
rs11800990	1.00[JPT][hapmap]
rs11807146	0.94[ASW][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12087032	1.00[CHD][hapmap]
rs12239929	1.00[JPT][hapmap]
rs1321670	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1321671	1.00[JPT][hapmap]
rs1322359	1.00[CHD][hapmap]
rs13374445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1407426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1407428	1.00[JPT][hapmap]
rs1407429	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1407430	1.00[CHD][hapmap]
rs1407431	0.85[CHD][hapmap]
rs1555494	1.00[JPT][hapmap]
rs16824465	1.00[JPT][hapmap]
rs16824488	1.00[JPT][hapmap]
rs16824564	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs16824576	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17447869	1.00[CHD][hapmap];0.80[GIH][hapmap]
rs17448216	1.00[CHD][hapmap];0.80[GIH][hapmap]
rs17448230	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs17461534	0.94[CEU][hapmap];0.83[CHD][hapmap];0.81[EUR][1000 genomes]
rs17505819	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs1830622	1.00[JPT][hapmap]
rs2057381	0.85[ASN][1000 genomes]
rs2057382	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs2057383	0.85[ASN][1000 genomes]
rs2057384	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2057385	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[ASN][1000 genomes]
rs2129125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2220128	1.00[CHD][hapmap]
rs35425624	0.85[CHD][hapmap]
rs41357745	1.00[CHD][hapmap]
rs41458549	1.00[CHD][hapmap]
rs4651287	1.00[CHD][hapmap]
rs4651288	0.82[GIH][hapmap]
rs6425004	1.00[JPT][hapmap]
rs6425005	1.00[JPT][hapmap]
rs6657554	1.00[JPT][hapmap]
rs6657683	1.00[JPT][hapmap]
rs6660510	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs6662653	1.00[JPT][hapmap]
rs6667316	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];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6675465	1.00[JPT][hapmap]
rs6676522	1.00[JPT][hapmap]
rs6676629	1.00[JPT][hapmap]
rs6683809	1.00[JPT][hapmap]
rs6688298	1.00[JPT][hapmap]
rs6690475	1.00[JPT][hapmap]
rs6690559	1.00[JPT][hapmap]
rs6690714	1.00[JPT][hapmap]
rs6696804	1.00[JPT][hapmap]
rs6698721	1.00[JPT][hapmap]
rs726777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521401	1.00[JPT][hapmap]
rs7540773	1.00[JPT][hapmap]
rs7541361	1.00[JPT][hapmap]
rs7544533	1.00[JPT][hapmap]
rs7546152	1.00[JPT][hapmap]
rs900775	0.85[CHD][hapmap]
rs9425349	0.83[CEU][hapmap]

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
rs12078444	NMNAT2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185850400-185863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:185851000-185855800	Weak transcription	Liver	Liver
3	chr1:185854800-185855600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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