Variant report

Variant	rs34279227
Chromosome Location	chr3:98633285-98633286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98619470..98621395-chr3:98630359..98633693,3	MCF-7	breast:
2	chr17:57919674..57922229-chr3:98633169..98634718,2	MCF-7	breast:
3	chr3:98631689..98634249-chr3:98634702..98637082,3	MCF-7	breast:
4	chr3:98620790..98623789-chr3:98631975..98634089,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction
ENSG00000239462	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10428160	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10589669	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11552978	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12107272	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12108018	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12108142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13059624	0.87[EUR][1000 genomes]
rs13065136	0.98[EUR][1000 genomes]
rs13068317	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072410	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13074614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074787	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13076960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078549	0.93[EUR][1000 genomes]
rs13079960	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13080057	0.87[EUR][1000 genomes]
rs13081992	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13083613	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13083934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13084692	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13087627	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13087631	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13088532	0.89[EUR][1000 genomes]
rs13091170	0.98[EUR][1000 genomes]
rs13091236	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13091956	0.82[EUR][1000 genomes]
rs13093128	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096085	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13097876	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100915	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100937	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1983009	0.84[EUR][1000 genomes]
rs2439232	0.91[EUR][1000 genomes]
rs2454687	0.89[EUR][1000 genomes]
rs34008360	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34269725	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34284740	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34394867	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34428696	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34458031	0.91[AMR][1000 genomes]
rs34470469	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34479374	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34489202	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34688367	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34711372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34725039	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34791359	0.91[AMR][1000 genomes]
rs34826460	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34848749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860591	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35006699	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35025156	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35076733	0.93[EUR][1000 genomes]
rs35098355	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35103318	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35219252	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35234681	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35239055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35312318	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35366262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35422064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35499232	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35514544	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35526367	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35539438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35592768	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35764973	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35854439	0.82[EUR][1000 genomes]
rs35894621	0.91[AMR][1000 genomes]
rs35914268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35947493	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35947806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36028944	0.82[AMR][1000 genomes]
rs36032715	0.87[EUR][1000 genomes]
rs36098932	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36157152	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36160001	0.84[EUR][1000 genomes]
rs36175276	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41267851	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55644421	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56083233	0.98[EUR][1000 genomes]
rs56094988	0.82[EUR][1000 genomes]
rs56246599	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56408882	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6764579	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6805362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71124004	0.83[EUR][1000 genomes]
rs71311393	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311394	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311397	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71311398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71311402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71313504	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313506	0.91[EUR][1000 genomes]
rs71313508	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313509	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313510	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313511	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313512	0.91[AMR][1000 genomes]
rs7614053	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98623600-98636400	Weak transcription	Fetal Heart	heart
2	chr3:98625400-98636600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:98625600-98637200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:98626400-98634400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:98626600-98641600	Weak transcription	NHLF	lung
6	chr3:98632000-98634200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:98632800-98633600	Enhancers	HepG2	liver
8	chr3:98632800-98634600	Flanking Active TSS	A549	lung
9	chr3:98632800-98635200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:98633000-98633400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:98633000-98633600	Enhancers	Liver	Liver
12	chr3:98633000-98633800	Enhancers	NH-A	brain
13	chr3:98633000-98634800	Enhancers	Osteobl	bone
14	chr3:98633200-98633400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:98633200-98633400	Enhancers	HMEC	breast
16	chr3:98633200-98633600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:98633200-98633600	Bivalent Enhancer	K562	blood
18	chr3:98633200-98635000	Enhancers	Muscle Satellite Cultured Cells	--

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