Variant report

Variant	rs12908028
Chromosome Location	chr15:51890663-51890664
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51890344..51891914-chr15:51895307..51897128,2	MCF-7	breast:
2	chr15:51887877..51891217-chr15:51913532..51916427,5	MCF-7	breast:
3	chr15:51889282..51891197-chr15:51892580..51894608,3	K562	blood:
4	chr15:51890575..51893742-chr15:52120649..52123561,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11070850	0.85[EUR][1000 genomes]
rs11855041	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592390	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12592422	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17704742	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869930	0.92[EUR][1000 genomes]
rs2414104	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2414108	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445751	0.80[CHB][hapmap]
rs2470192	0.84[CHB][hapmap]
rs2470194	0.85[CHB][hapmap]
rs2607111	0.92[EUR][1000 genomes]
rs2607113	0.90[EUR][1000 genomes]
rs28362471	0.93[EUR][1000 genomes]
rs34604744	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4359386	0.95[EUR][1000 genomes]
rs4436729	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4462536	0.95[EUR][1000 genomes]
rs4775945	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs4775950	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775967	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493498	0.90[CHB][hapmap]
rs6493502	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493504	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164999	0.92[EUR][1000 genomes]
rs7176988	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8024233	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8025536	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8030113	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8034340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs930919	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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
rs12908028	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51875400-51891400	Weak transcription	K562	blood
2	chr15:51889400-51891400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:51889400-51891400	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr15:51889400-51909400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:51890000-51891800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:51890000-51894800	Weak transcription	Gastric	stomach
7	chr15:51890000-51902000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:51890200-51891400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr15:51890400-51890800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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