Variant report

Variant	rs1407429
Chromosome Location	chr1:185755754-185755755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185744979..185747367-chr1:185754929..185757056,2	K562	blood:
2	chr1:185755489..185757361-chr1:185758549..185760454,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

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[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10911785	1.00[JPT][hapmap]
rs10911789	1.00[JPT][hapmap]
rs1124757	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11581777	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs11583867	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11800990	1.00[JPT][hapmap]
rs11807146	0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12057982	0.91[EUR][1000 genomes]
rs12063964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078015	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078444	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12079064	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12083564	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12085167	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12087032	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes]
rs12098116	0.84[EUR][1000 genomes]
rs12239929	1.00[JPT][hapmap]
rs1321668	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1321669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1321670	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321671	1.00[JPT][hapmap]
rs1322359	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1322362	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1322364	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13374445	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13376668	0.81[EUR][1000 genomes]
rs1407426	1.00[JPT][hapmap]
rs1407428	1.00[JPT][hapmap]
rs1407430	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes]
rs1407431	0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1552281	0.89[ASN][1000 genomes]
rs1555494	1.00[JPT][hapmap]
rs16824465	1.00[JPT][hapmap]
rs16824488	1.00[JPT][hapmap]
rs16824516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824564	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]
rs16824576	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17446906	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17447869	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs17448202	0.89[EUR][1000 genomes]
rs17448216	0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs17448230	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];0.91[EUR][1000 genomes]
rs17461534	0.83[CHD][hapmap]
rs17505819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17507044	0.81[EUR][1000 genomes]
rs17507170	0.89[EUR][1000 genomes]
rs1830622	1.00[JPT][hapmap]
rs1951517	0.91[CEU][hapmap]
rs2057381	0.89[EUR][1000 genomes]
rs2057382	0.95[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2057383	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2057384	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2057385	0.95[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2129125	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2170859	0.95[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2220128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35314812	0.84[EUR][1000 genomes]
rs35425624	0.87[CEU][hapmap];0.85[CHD][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs41357745	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs41458549	1.00[CHD][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs4515745	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4593772	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4596837	0.89[ASN][1000 genomes]
rs4651287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651288	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs57398679	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57686227	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61829860	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61829884	0.81[EUR][1000 genomes]
rs61831528	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61831532	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425004	1.00[JPT][hapmap]
rs6425005	1.00[JPT][hapmap]
rs6657554	1.00[JPT][hapmap]
rs6657683	1.00[JPT][hapmap]
rs6660510	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6662653	1.00[JPT][hapmap]
rs6667316	1.00[CHB][hapmap];1.00[JPT][hapmap]
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]
rs6692479	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696804	1.00[JPT][hapmap]
rs6698721	1.00[JPT][hapmap]
rs726777	1.00[JPT][hapmap]
rs7414598	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7521401	1.00[JPT][hapmap]
rs7540773	1.00[JPT][hapmap]
rs7541361	1.00[JPT][hapmap]
rs7544533	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546152	1.00[JPT][hapmap]
rs900775	0.85[CHD][hapmap]
rs9628625	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs994970	0.85[YRI][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
rs1407429	NMNAT2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185737800-185758800	Weak transcription	Fetal Lung	lung
2	chr1:185747400-185756400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:185753600-185757600	Weak transcription	Right Atrium	heart
4	chr1:185753600-185759600	Weak transcription	Pancreas	Pancrea
5	chr1:185754600-185756200	Weak transcription	Fetal Brain Male	brain
6	chr1:185755200-185756800	Enhancers	NHDF-Ad	bronchial
7	chr1:185755200-185758800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:185755200-185759400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:185755200-185760000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:185755400-185756600	Enhancers	Osteobl	bone
11	chr1:185755400-185766600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:185755600-185756800	Enhancers	Aorta	Aorta

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