Variant report

Variant	rs7173725
Chromosome Location	chr15:52378750-52378751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52377841..52381890-chr15:52385392..52388503,3	MCF-7	breast:
2	chr15:52366885..52371007-chr15:52377121..52381657,4	MCF-7	breast:
3	chr15:52377651..52380251-chr15:52438624..52441229,2	MCF-7	breast:
4	chr15:52377947..52381389-chr15:52382632..52385327,3	MCF-7	breast:
5	chr15:52373505..52375640-chr15:52378601..52380310,2	MCF-7	breast:
6	chr15:52310492..52312947-chr15:52377294..52381782,5	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK6-2	chr15:52378514-52378754	XLOC_011252
2	lnc-MAPK6-2	chr15:52378514-52378771	ENSG00000259178.1

No data

No data

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259178	Chromatin interaction
ENSG00000242327	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10518674	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs12050787	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438375	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439046	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706513	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414127	0.88[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs36046047	0.81[TSI][hapmap]
rs4627278	0.81[TSI][hapmap]
rs4775999	0.81[TSI][hapmap]
rs55931072	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58510474	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58555938	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72732980	0.87[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	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1039841	chr15:52357448-52381377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52371600-52378800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:52373200-52378800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:52377800-52384800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:52378400-52379600	ZNF genes & repeats	GM12878-XiMat	blood
5	chr15:52378600-52379000	ZNF genes & repeats	HUVEC	blood vessel
6	chr15:52378600-52379000	ZNF genes & repeats	NHEK	skin
7	chr15:52378600-52379600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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