Variant report

Variant	rs2399405
Chromosome Location	chr3:111869012-111869013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10511309	0.89[ASN][1000 genomes]
rs10934138	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10934158	0.80[EUR][1000 genomes]
rs1119338	0.80[EUR][1000 genomes]
rs11712289	0.80[EUR][1000 genomes]
rs11714145	0.80[EUR][1000 genomes]
rs11714273	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719485	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11914637	0.97[ASN][1000 genomes]
rs11928353	0.83[ASN][1000 genomes]
rs12054138	0.86[ASN][1000 genomes]
rs12493824	0.89[ASN][1000 genomes]
rs12494678	0.80[EUR][1000 genomes]
rs12629465	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12634031	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13060187	0.89[ASN][1000 genomes]
rs13064510	0.89[ASN][1000 genomes]
rs13067030	0.82[ASN][1000 genomes]
rs13069887	0.89[ASN][1000 genomes]
rs13079745	0.89[ASN][1000 genomes]
rs13088733	0.94[ASN][1000 genomes]
rs13314268	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13314792	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13315900	0.87[ASN][1000 genomes]
rs13327160	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13327165	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1492482	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1492487	0.84[EUR][1000 genomes]
rs1586875	0.80[EUR][1000 genomes]
rs1602670	0.97[ASN][1000 genomes]
rs1602671	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1844995	0.80[EUR][1000 genomes]
rs2029636	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2029637	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2046983	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2087767	0.91[ASN][1000 genomes]
rs2087768	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131232	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2131233	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2172314	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2172315	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3929356	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3995955	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4352358	0.83[ASN][1000 genomes]
rs4438629	0.89[ASN][1000 genomes]
rs4449289	0.80[EUR][1000 genomes]
rs4528910	0.80[EUR][1000 genomes]
rs4568109	0.80[EUR][1000 genomes]
rs4568110	0.80[EUR][1000 genomes]
rs4577433	0.89[ASN][1000 genomes]
rs4586779	0.91[ASN][1000 genomes]
rs4682086	0.90[ASN][1000 genomes]
rs4682090	0.91[ASN][1000 genomes]
rs4682361	0.95[ASN][1000 genomes]
rs4682365	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682372	0.83[ASN][1000 genomes]
rs4682374	0.83[ASN][1000 genomes]
rs5013874	0.80[EUR][1000 genomes]
rs56852402	0.80[EUR][1000 genomes]
rs60443450	0.80[EUR][1000 genomes]
rs62277462	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62279470	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6438039	0.89[ASN][1000 genomes]
rs6763462	0.80[EUR][1000 genomes]
rs6764248	0.87[ASN][1000 genomes]
rs6766122	0.80[EUR][1000 genomes]
rs6766622	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766996	0.89[ASN][1000 genomes]
rs6767017	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67704344	0.91[ASN][1000 genomes]
rs6773161	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6784524	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791042	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792318	0.80[EUR][1000 genomes]
rs6805795	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6807950	0.80[EUR][1000 genomes]
rs6808920	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611019	0.80[EUR][1000 genomes]
rs7614211	0.80[EUR][1000 genomes]
rs7616020	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7622733	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7642447	0.80[EUR][1000 genomes]
rs7642496	0.80[EUR][1000 genomes]
rs7646742	0.80[EUR][1000 genomes]
rs9288937	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9288938	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9288943	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs958695	0.83[ASN][1000 genomes]
rs9809196	0.80[EUR][1000 genomes]
rs9818716	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9821935	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9827793	0.80[EUR][1000 genomes]
rs9827894	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9828290	0.80[EUR][1000 genomes]
rs9829464	0.80[EUR][1000 genomes]
rs9835431	0.85[AFR][1000 genomes]
rs9837375	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844769	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9851173	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9859163	0.80[EUR][1000 genomes]
rs9861756	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9864872	0.80[EUR][1000 genomes]
rs9871650	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9872691	0.80[EUR][1000 genomes]
rs9875860	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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	nsv1010219	chr3:111856709-111923647	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv3323712	chr3:111861311-111890479	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111866200-111875800	Weak transcription	Right Ventricle	heart
2	chr3:111867200-111869200	ZNF genes & repeats	HMEC	breast
3	chr3:111867400-111869200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:111867600-111869400	ZNF genes & repeats	Left Ventricle	heart
5	chr3:111867800-111869400	Enhancers	NHEK	skin
6	chr3:111868800-111869800	Weak transcription	Fetal Stomach	stomach
7	chr3:111868800-111869800	Weak transcription	Gastric	stomach
8	chr3:111868800-111871800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:111869000-111878400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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