Variant report

Variant	rs1693489
Chromosome Location	chr15:52770172-52770173
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	chr15:52769299..52770984-chr15:52860581..52862145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1614200	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1724637	0.82[AFR][1000 genomes]
rs2453986	0.91[AMR][1000 genomes]
rs8027927	0.82[AMR][1000 genomes]
rs8028425	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1693489	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs1693489	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52757200-52770400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:52757400-52771800	Weak transcription	Primary T cells from cord blood	blood
3	chr15:52758600-52772000	Weak transcription	HUVEC	blood vessel
4	chr15:52758600-52773000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:52758800-52773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:52759000-52772000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:52759200-52770600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:52759200-52771000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:52759200-52778200	Weak transcription	Right Atrium	heart
10	chr15:52759400-52773000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:52759800-52773000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:52760400-52770600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:52764200-52773000	Weak transcription	Brain Anterior Caudate	brain
14	chr15:52767600-52773600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:52769800-52770800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:52769800-52774400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:52770000-52771200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:52770000-52772600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:52770000-52776600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr15:52770000-52777000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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