Variant report

Variant	rs4651287
Chromosome Location	chr1:185716964-185716965
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185708096..185710876-chr1:185716929..185719553,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10911781	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1124757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579889	0.83[ASN][1000 genomes]
rs11581777	0.95[CEU][hapmap]
rs11583092	0.83[ASN][1000 genomes]
rs11583867	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11807146	0.95[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12057982	0.80[EUR][1000 genomes]
rs12063964	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12078015	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12078444	1.00[CHD][hapmap]
rs12079064	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12083564	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085167	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12087032	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs1321668	0.94[ASN][1000 genomes]
rs1321669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322359	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322362	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1322364	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13374445	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs13376668	0.85[EUR][1000 genomes]
rs1407429	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]
rs1407430	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs1407431	0.95[CEU][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs1552281	0.94[ASN][1000 genomes]
rs16824390	0.83[ASN][1000 genomes]
rs16824396	0.83[ASN][1000 genomes]
rs16824516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824564	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs16824576	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs17445778	0.83[ASN][1000 genomes]
rs17446906	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17447869	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap]
rs17448216	0.95[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap]
rs17448230	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs17461534	0.83[CHD][hapmap]
rs17505819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17507044	0.85[EUR][1000 genomes]
rs1951517	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2057382	0.95[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2057383	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2057384	0.81[EUR][1000 genomes]
rs2057385	0.95[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap]
rs2129125	1.00[CEU][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2170859	0.95[CEU][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2220128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35314812	0.88[EUR][1000 genomes]
rs35425624	0.87[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41357745	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs41458549	1.00[CHD][hapmap]
rs4515745	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4593772	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4596837	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651288	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs57398679	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61290318	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61829860	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61829884	0.85[EUR][1000 genomes]
rs61831470	0.83[ASN][1000 genomes]
rs61831483	0.83[ASN][1000 genomes]
rs61831485	0.83[ASN][1000 genomes]
rs61831486	0.83[ASN][1000 genomes]
rs61831502	0.83[ASN][1000 genomes]
rs61831503	0.83[ASN][1000 genomes]
rs61831505	0.83[ASN][1000 genomes]
rs61831519	0.82[ASN][1000 genomes]
rs61831528	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61831532	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6660510	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6667316	1.00[CHB][hapmap]
rs6692479	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7414598	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544533	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900775	0.85[CHD][hapmap];0.84[TSI][hapmap]
rs9628625	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs994970	0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv2753636	chr1:185706947-185734487	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4651287	NMNAT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185705200-185717000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:185712800-185717000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:185715000-185721000	Weak transcription	Aorta	Aorta

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