Variant report

Variant	rs45539339
Chromosome Location	chr7:87071530-87071531
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86972942..86975537-chr7:87069538..87072015,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000005469	Chromatin interaction
ENSG00000182165	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1017054	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034821	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487804	0.82[EUR][1000 genomes]
rs11761050	0.82[EUR][1000 genomes]
rs11767995	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768036	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11768699	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773089	0.82[EUR][1000 genomes]
rs17149539	0.82[EUR][1000 genomes]
rs17149547	0.82[EUR][1000 genomes]
rs17149601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17149606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230028	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35737120	0.82[EUR][1000 genomes]
rs4148829	0.82[EUR][1000 genomes]
rs45437295	0.82[EUR][1000 genomes]
rs45443210	0.82[EUR][1000 genomes]
rs45466200	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45473093	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45474405	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45503798	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45505301	0.82[EUR][1000 genomes]
rs45517839	0.82[EUR][1000 genomes]
rs45521742	0.82[EUR][1000 genomes]
rs45533331	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45540936	0.82[EUR][1000 genomes]
rs45543841	0.82[EUR][1000 genomes]
rs45547639	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45549532	0.82[EUR][1000 genomes]
rs45549641	0.81[EUR][1000 genomes]
rs45552832	0.82[EUR][1000 genomes]
rs45579433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45609336	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956661	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957680	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6977539	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6977739	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788404	0.82[EUR][1000 genomes]
rs7807638	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1029486	chr7:86856387-87121976	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv539004	chr7:86856387-87121976	Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1828294	chr7:86857553-87147397	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv1024376	chr7:86905796-87129346	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv888678	chr7:86932085-87101407	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	esv3382480	chr7:87031452-87133648	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv464623	chr7:87040629-87139316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv607726	chr7:87040629-87139316	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv888679	chr7:87057699-87101407	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv888680	chr7:87065687-87101407	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv888681	chr7:87068464-87101407	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv888682	chr7:87068464-87103263	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	esv1792643	chr7:87069758-87108420	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86980000-87085600	Weak transcription	Right Ventricle	heart
2	chr7:87019800-87079400	Strong transcription	Liver	Liver
3	chr7:87024800-87093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:87040800-87072400	Weak transcription	Aorta	Aorta
5	chr7:87040800-87085600	Weak transcription	Psoas Muscle	Psoas
6	chr7:87047000-87078000	Strong transcription	Primary B cells from cord blood	blood
7	chr7:87051200-87085600	Weak transcription	Fetal Heart	heart
8	chr7:87052200-87072000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:87055800-87075000	Weak transcription	GM12878-XiMat	blood
10	chr7:87056200-87075200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr7:87064600-87077800	Weak transcription	Spleen	Spleen
12	chr7:87065000-87077800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:87066800-87072000	Weak transcription	HepG2	liver
14	chr7:87066800-87085600	Weak transcription	Left Ventricle	heart
15	chr7:87069200-87071800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:87069400-87071800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:87070400-87072800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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