Variant report

Variant	rs900775
Chromosome Location	chr1:185689139-185689140
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	chr1:185687976..185689739-chr1:186121174..186123816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143341	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10911781	0.85[CHD][hapmap]
rs11579889	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583092	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583867	1.00[CHB][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs11584252	0.94[EUR][1000 genomes]
rs11587852	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589543	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11807146	0.84[TSI][hapmap]
rs12078015	0.84[ASN][1000 genomes]
rs12078444	0.85[CHD][hapmap]
rs12079064	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12083564	0.84[ASN][1000 genomes]
rs12085167	0.84[ASN][1000 genomes]
rs12087032	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[TSI][hapmap]
rs1321668	0.84[ASN][1000 genomes]
rs1322359	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs1322364	0.84[ASN][1000 genomes]
rs1358871	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1407429	0.85[CHD][hapmap]
rs1407430	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[TSI][hapmap]
rs1407431	1.00[CHB][hapmap];0.89[TSI][hapmap]
rs1484134	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1484135	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552281	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824390	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16824396	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16824564	0.85[CHD][hapmap]
rs16824576	0.85[CHD][hapmap]
rs17445778	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17446906	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs17447869	0.85[CHD][hapmap]
rs17448216	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17448230	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17505819	0.85[CHD][hapmap]
rs1951517	1.00[CHB][hapmap]
rs2004324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057382	0.85[CHD][hapmap];0.89[TSI][hapmap]
rs2057385	0.85[CHD][hapmap]
rs2170859	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2220128	0.85[CHD][hapmap];0.84[TSI][hapmap]
rs34923020	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35425624	1.00[CHB][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41357745	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs41519044	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4515745	0.84[ASN][1000 genomes]
rs4593772	0.84[ASN][1000 genomes]
rs4596837	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4651287	0.85[CHD][hapmap];0.84[TSI][hapmap]
rs55993167	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56031313	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56238699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57146145	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58708412	0.95[EUR][1000 genomes]
rs59197925	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59253277	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59702468	0.94[EUR][1000 genomes]
rs60074235	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60376365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61829644	0.86[EUR][1000 genomes]
rs61829860	0.84[ASN][1000 genomes]
rs61831462	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61831464	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61831470	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831480	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61831482	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61831483	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831484	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61831485	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831486	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831502	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831503	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831504	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61831505	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61831519	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61831521	0.87[EUR][1000 genomes]
rs61831528	0.84[ASN][1000 genomes]
rs61831532	0.84[ASN][1000 genomes]
rs6656530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs6660510	0.85[CHD][hapmap]
rs6668606	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6668607	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6692602	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72727759	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7414598	0.84[ASN][1000 genomes]
rs7534755	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7538168	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7544533	0.81[TSI][hapmap]
rs7547022	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7554903	0.95[EUR][1000 genomes]
rs9286857	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936723	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9628625	1.00[CHB][hapmap]
rs992760	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.84[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
rs900775	NMNAT2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185683000-185702600	Weak transcription	Aorta	Aorta
2	chr1:185686800-185690400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:185687000-185689600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:185687400-185689400	Enhancers	NHDF-Ad	bronchial
5	chr1:185687400-185690000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:185687600-185689400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:185687600-185689800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:185687800-185689200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:185688200-185689200	Enhancers	Liver	Liver
10	chr1:185688400-185691200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:185688600-185689600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:185688600-185690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:185688600-185690800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:185688800-185689800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:185688800-185689800	Enhancers	HMEC	breast
16	chr1:185688800-185689800	Weak transcription	Osteobl	bone
17	chr1:185688800-185690200	Enhancers	NHEK	skin
18	chr1:185688800-185691200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:185688800-185703000	Weak transcription	NH-A	brain

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