Variant report

Variant	rs12592390
Chromosome Location	chr15:51869645-51869646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51857366..51859999-chr15:51867554..51870226,2	MCF-7	breast:
2	chr15:51867811..51869730-chr15:51913400..51915633,2	MCF-7	breast:
3	chr15:51869314..51872893-chr15:51913496..51916376,3	MCF-7	breast:
4	chr15:51867858..51870463-chr15:51910952..51912815,2	K562	blood:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10467923	0.81[JPT][hapmap]
rs11070850	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070852	0.88[ASN][1000 genomes]
rs11070862	0.81[CHB][hapmap]
rs11855041	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908028	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17648128	0.82[CHB][hapmap]
rs17704742	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1869930	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2258064	0.81[EUR][1000 genomes]
rs2414104	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414108	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2445746	0.86[CHB][hapmap]
rs2445751	0.87[CHB][hapmap]
rs2470192	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2470194	0.91[CHB][hapmap]
rs2607111	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2607113	0.89[EUR][1000 genomes]
rs28362471	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34604744	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4359386	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4436729	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4462536	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4775945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775950	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775967	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493498	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs6493502	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493504	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164999	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7176988	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024233	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8025536	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030113	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030534	0.86[ASN][1000 genomes]
rs8034340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs898135	0.86[CHB][hapmap]
rs930919	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv904218	chr15:51743186-51873407	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv569405	chr15:51791559-51890282	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv457138	chr15:51838719-51890282	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv569406	chr15:51838719-51890282	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
8	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
9	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
10	nsv569408	chr15:51867172-51946100	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12592390	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51867800-51872400	Enhancers	K562	blood
2	chr15:51868200-51870200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr15:51868200-51870800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:51868600-51869800	Enhancers	NHEK	skin
5	chr15:51868600-51870200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:51868600-51870200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:51868600-51870200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:51868600-51870400	Enhancers	Hela-S3	cervix
9	chr15:51868600-51872000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr15:51868800-51870800	Enhancers	Colon Smooth Muscle	Colon
11	chr15:51869000-51870200	Enhancers	Adipose Nuclei	Adipose
12	chr15:51869000-51871600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:51869200-51869800	Active TSS	Primary B cells from cord blood	blood
14	chr15:51869400-51869800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:51869400-51870000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:51869600-51870000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr15:51869600-51870800	Weak transcription	Small Intestine	intestine
18	chr15:51869600-51875200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr15:51869600-51889600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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