Variant report

Variant	rs28842558
Chromosome Location	chr7:7596817-7596818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:7596698-7596867	A549	lung:	n/a	n/a
2	POLR2A	chr7:7596537-7596902	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7594653..7598119-chr7:7605065..7607916,4	MCF-7	breast:
2	chr7:7473373..7475762-chr7:7594753..7597282,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272732	TF binding region
ENSG00000272894	TF binding region
ENSG00000164654	Chromatin interaction
ENSG00000272894	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10085615	1.00[AMR][1000 genomes]
rs10085678	1.00[AMR][1000 genomes]
rs10224056	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10226442	1.00[AMR][1000 genomes]
rs10227544	1.00[AMR][1000 genomes]
rs10237888	1.00[AMR][1000 genomes]
rs10242691	1.00[AMR][1000 genomes]
rs10244335	1.00[AMR][1000 genomes]
rs10244366	1.00[AMR][1000 genomes]
rs10244757	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10246309	1.00[AMR][1000 genomes]
rs10247226	1.00[AMR][1000 genomes]
rs10255581	1.00[AMR][1000 genomes]
rs10257117	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10257279	1.00[AMR][1000 genomes]
rs10257458	1.00[AMR][1000 genomes]
rs10258922	1.00[AMR][1000 genomes]
rs10259911	1.00[AMR][1000 genomes]
rs10262309	1.00[AMR][1000 genomes]
rs10266393	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10267405	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10269709	1.00[AMR][1000 genomes]
rs10278024	1.00[AMR][1000 genomes]
rs10282183	1.00[AMR][1000 genomes]
rs12333875	1.00[AMR][1000 genomes]
rs12334276	1.00[AMR][1000 genomes]
rs17168530	1.00[AMR][1000 genomes]
rs28442228	1.00[AMR][1000 genomes]
rs28535494	1.00[AMR][1000 genomes]
rs28565038	1.00[AMR][1000 genomes]
rs28602992	1.00[AMR][1000 genomes]
rs28681690	1.00[AMR][1000 genomes]
rs28712138	1.00[AMR][1000 genomes]
rs6951703	1.00[AMR][1000 genomes]
rs7778417	1.00[AMR][1000 genomes]
rs7791164	1.00[AMR][1000 genomes]
rs7805479	1.00[AMR][1000 genomes]
rs7810456	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers 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	42 gene(s)	inside rSNPs	diseases
15	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
16	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7589400-7605800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:7590000-7606000	Weak transcription	Brain Substantia Nigra	brain
3	chr7:7590000-7606200	Weak transcription	Ovary	ovary
4	chr7:7590200-7605800	Weak transcription	Brain Anterior Caudate	brain
5	chr7:7590200-7605800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:7592400-7599200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:7593800-7606000	Weak transcription	Right Atrium	heart
8	chr7:7594400-7597000	Enhancers	Brain Germinal Matrix	brain
9	chr7:7595200-7597600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:7595200-7603000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr7:7595200-7603600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:7595800-7598800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:7595800-7605600	Weak transcription	Fetal Kidney	kidney
14	chr7:7596200-7597400	Genic enhancers	Pancreas	Pancrea
15	chr7:7596400-7597000	Enhancers	Lung	lung
16	chr7:7596400-7603200	Weak transcription	Aorta	Aorta
17	chr7:7596600-7597200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:7596600-7597200	Genic enhancers	Gastric	stomach
19	chr7:7596800-7597000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:7596800-7602800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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