Variant report

Variant	rs2878611
Chromosome Location	chr4:7373775-7373776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7193444..7195418-chr4:7373102..7374832,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184985	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10029954	0.80[ASN][1000 genomes]
rs12503542	0.95[MEX][hapmap]
rs12503600	0.80[CEU][hapmap];0.91[MEX][hapmap]
rs2878610	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878612	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3864206	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs3864207	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864210	0.80[CEU][hapmap];0.95[MEX][hapmap]
rs3864218	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs3965270	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4044945	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4044946	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4689109	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4689712	0.80[CEU][hapmap];0.95[MEX][hapmap]
rs4689713	0.80[CEU][hapmap];0.95[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv432556	chr4:7174993-7391948	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv878546	chr4:7285356-7376694	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv878547	chr4:7289113-7376694	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv878549	chr4:7295154-7376694	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv878551	chr4:7297506-7376694	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1011547	chr4:7318232-7637410	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv537017	chr4:7318232-7637410	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1003679	chr4:7319111-7449262	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv878553	chr4:7321511-7376694	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv878559	chr4:7353052-7376694	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1012289	chr4:7361958-7395292	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv469758	chr4:7370083-7546250	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7368200-7383000	Weak transcription	Right Atrium	heart
2	chr4:7370200-7376600	Weak transcription	Brain Substantia Nigra	brain
3	chr4:7370400-7376200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:7370400-7377000	Weak transcription	Fetal Lung	lung
5	chr4:7371200-7373800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr4:7371600-7374000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr4:7372400-7374000	Enhancers	NH-A	brain
8	chr4:7372600-7377000	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:7372800-7373800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:7372800-7373800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:7372800-7373800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:7372800-7373800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:7372800-7373800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr4:7372800-7373800	Enhancers	HSMM	muscle
15	chr4:7372800-7374000	Enhancers	Fetal Stomach	stomach
16	chr4:7372800-7376200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:7373000-7377000	Weak transcription	Brain Angular Gyrus	brain
18	chr4:7373000-7383400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:7373400-7373800	Enhancers	Brain Germinal Matrix	brain
20	chr4:7373400-7373800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:7373600-7373800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:7373600-7377000	Weak transcription	Ovary	ovary

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