Variant report

Variant	rs10258922
Chromosome Location	chr7:7590280-7590281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
2	chr7:7588174..7592470-chr7:7605427..7608009,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL28A1-1	chr7:7589264-7591107	XLOC_006350
2	lnc-COL28A1-1	chr7:7589735-7591107	NR_110084
3	lnc-COL28A1-1	chr7:7589735-7591107	ENSG00000272732.1

Variant related genes	Relation type
ENSG00000164654	Chromatin interaction
ENSG00000272894	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10085615	1.00[AMR][1000 genomes]
rs10085678	1.00[AMR][1000 genomes]
rs10224056	1.00[AMR][1000 genomes]
rs10226442	0.90[AFR][1000 genomes];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[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10244366	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10244757	1.00[AMR][1000 genomes]
rs10246309	1.00[AMR][1000 genomes]
rs10247226	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10255581	1.00[AMR][1000 genomes]
rs10257117	1.00[AMR][1000 genomes]
rs10257279	1.00[AMR][1000 genomes]
rs10257458	1.00[AMR][1000 genomes]
rs10259911	1.00[AMR][1000 genomes]
rs10262309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10266393	1.00[AMR][1000 genomes]
rs10267405	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[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17168530	1.00[AMR][1000 genomes]
rs28442228	1.00[AMR][1000 genomes]
rs28535494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28565038	1.00[AMR][1000 genomes]
rs28602992	1.00[AMR][1000 genomes]
rs28628287	1.00[AFR][1000 genomes]
rs28681690	1.00[AMR][1000 genomes]
rs28712138	1.00[AMR][1000 genomes]
rs28842558	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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7575800-7593000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7581800-7595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:7588000-7591200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:7588000-7592200	Weak transcription	HSMM	muscle
5	chr7:7588600-7590400	Weak transcription	Liver	Liver
6	chr7:7589400-7605800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:7589600-7590600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr7:7589800-7596000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:7589800-7596000	Weak transcription	Aorta	Aorta
10	chr7:7589800-7596000	Weak transcription	Placenta	Placenta
11	chr7:7589800-7596600	Weak transcription	Gastric	stomach
12	chr7:7590000-7591600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr7:7590000-7593600	Weak transcription	Brain Angular Gyrus	brain
14	chr7:7590000-7595000	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:7590000-7606000	Weak transcription	Brain Substantia Nigra	brain
16	chr7:7590000-7606200	Weak transcription	Ovary	ovary
17	chr7:7590200-7605800	Weak transcription	Brain Anterior Caudate	brain
18	chr7:7590200-7605800	Weak transcription	Brain Inferior Temporal Lobe	brain

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