Variant report

Variant	rs4302343
Chromosome Location	chr3:139225545-139225546
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139153603..139154270-chr3:139225278..139226293,3	MCF-7	breast:
2	chr3:139219930..139221523-chr3:139223151..139225798,2	K562	blood:
3	chr3:139146075..139147113-chr3:139225388..139226287,6	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1017469	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10935322	0.82[AMR][1000 genomes]
rs10935326	0.84[AMR][1000 genomes]
rs10935328	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11705700	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11706576	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11717119	0.82[AMR][1000 genomes]
rs11721246	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11928377	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12495890	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13064670	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13313904	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13316469	0.84[AMR][1000 genomes]
rs13326837	0.82[AMR][1000 genomes]
rs13327001	0.82[AMR][1000 genomes]
rs13327467	0.82[AMR][1000 genomes]
rs1371338	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1371339	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1550352	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1583743	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1586862	0.82[AMR][1000 genomes]
rs17395255	0.82[AMR][1000 genomes]
rs17395262	0.82[AMR][1000 genomes]
rs17395304	0.82[AMR][1000 genomes]
rs176984	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1817830	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1817831	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs188422	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs192687	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211582	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211585	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2118980	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2289347	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2289349	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2349058	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28771131	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28780368	0.84[AMR][1000 genomes]
rs28829348	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28861812	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs295472	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295480	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs295483	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295486	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295488	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34680708	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3555	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35674260	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs387987	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3888890	0.82[AMR][1000 genomes]
rs4428138	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs444264	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4547659	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4563370	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683608	0.86[AFR][1000 genomes]
rs62270814	0.84[AMR][1000 genomes]
rs62270815	0.84[AMR][1000 genomes]
rs62270816	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6439858	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6439861	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6439862	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6778992	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6782957	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6801875	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6804877	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7372124	0.82[AMR][1000 genomes]
rs7372551	0.84[AMR][1000 genomes]
rs7372813	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7373116	0.82[AMR][1000 genomes]
rs7373657	0.82[AMR][1000 genomes]
rs7374065	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7374317	0.82[AMR][1000 genomes]
rs7374348	0.82[AMR][1000 genomes]
rs7433335	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7612112	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7616025	0.84[AMR][1000 genomes]
rs7626658	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627718	0.84[AMR][1000 genomes]
rs7645307	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs878535	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9289574	0.82[AMR][1000 genomes]
rs9289579	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964226	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs978835	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9812991	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9813503	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9817963	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9821875	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9821891	0.82[AMR][1000 genomes]
rs9828954	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9831144	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9833460	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9839681	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9848959	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9849255	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9850987	0.82[AMR][1000 genomes]
rs9851318	0.82[AMR][1000 genomes]
rs9857390	0.82[AMR][1000 genomes]
rs9859393	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9868900	0.82[AMR][1000 genomes]
rs9869745	0.82[AMR][1000 genomes]
rs9871030	0.82[AMR][1000 genomes]
rs9872749	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9873011	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9874227	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9876640	0.84[AMR][1000 genomes]
rs9879594	0.82[AMR][1000 genomes]
rs9881973	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9990108	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1001460	chr3:139194633-139241616	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139213200-139228400	Weak transcription	Gastric	stomach
3	chr3:139213400-139234200	Weak transcription	Ovary	ovary
4	chr3:139213400-139235600	Weak transcription	Pancreas	Pancrea
5	chr3:139213400-139235600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:139213400-139239000	Weak transcription	Brain Substantia Nigra	brain
7	chr3:139213600-139234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:139217400-139236000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:139223000-139247000	Weak transcription	Left Ventricle	heart
10	chr3:139224200-139227200	Enhancers	Duodenum Mucosa	Duodenum
11	chr3:139224200-139227400	Enhancers	Fetal Intestine Large	intestine
12	chr3:139224800-139227400	Enhancers	Fetal Intestine Small	intestine

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