Variant report

Variant	rs4955421
Chromosome Location	chr3:49218888-49218889
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	chr3:49193599..49196325-chr3:49216577..49219891,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10154992	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130183	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs12637346	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13084037	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082923	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs4292260	0.85[YRI][hapmap]
rs4384984	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955411	0.85[YRI][hapmap]
rs4955414	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955416	0.85[YRI][hapmap]
rs4955417	0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4955423	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs4955439	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446256	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	0.88[EUR][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7429661	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7617480	0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834003	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9867285	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4955421	NICN1-AS1	cis	Thyroid	GTEx
rs4955421	NICN1	cis	Thyroid	GTEx
rs4955421	AMT	cis	lung	GTEx
rs4955421	AMT	cis	Thyroid	GTEx
rs4955421	AMT	cis	Artery Aorta	GTEx
rs4955421	AMT	cis	Muscle Skeletal	GTEx
rs4955421	AMT	cis	Esophagus Mucosa	GTEx
rs4955421	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4955421	WDR6	cis	Nerve Tibial	GTEx
rs4955421	AMT	cis	Whole Blood	GTEx
rs4955421	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4955421	PFKFB4	cis	Nerve Tibial	GTEx
rs4955421	AMT	cis	Nerve Tibial	GTEx
rs4955421	WDR6	cis	Muscle Skeletal	GTEx
rs4955421	WDR6	cis	Heart Left Ventricle	GTEx
rs4955421	ARIH2	cis	Thyroid	GTEx
rs4955421	AMT	cis	Adipose Subcutaneous	GTEx
rs4955421	AMT	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:49214000-49219200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:49214000-49221400	Weak transcription	Liver	Liver
4	chr3:49214000-49224600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49214200-49220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:49214200-49224000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:49214800-49221400	Weak transcription	Fetal Lung	lung
8	chr3:49214800-49228600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:49215000-49225400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49215200-49221400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:49215600-49219200	Weak transcription	Lung	lung
12	chr3:49215600-49229000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:49216000-49220000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:49216000-49222800	Weak transcription	Fetal Intestine Small	intestine
15	chr3:49216200-49236400	Weak transcription	Esophagus	oesophagus
16	chr3:49216800-49219800	Weak transcription	Ovary	ovary
17	chr3:49216800-49220400	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:49217200-49220200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:49218800-49219000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:49218800-49219000	Enhancers	Fetal Kidney	kidney
21	chr3:49218800-49219400	Enhancers	HepG2	liver

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