Variant report

Variant	rs1456299
Chromosome Location	chr15:51982065-51982066
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51978743..51984253-chr15:51984583..51988197,6	MCF-7	breast:
2	chr15:51981798..51984182-chr15:51989191..51992186,3	K562	blood:
3	chr15:51971321..51974320-chr15:51980562..51984301,3	K562	blood:

Variant related genes	Relation type
ENSG00000259241	Chromatin interaction
ENSG00000104112	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10519313	0.83[CHB][hapmap]
rs11070863	0.90[ASN][1000 genomes]
rs11631725	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634955	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11637716	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11638106	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11638154	0.93[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1456300	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2168474	0.90[ASN][1000 genomes]
rs2278989	0.83[CHB][hapmap]
rs2278990	0.83[CHB][hapmap]
rs2305716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2622775	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2652594	0.94[JPT][hapmap]
rs28576876	0.92[ASN][1000 genomes]
rs4775968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55982453	0.92[ASN][1000 genomes]
rs60060794	0.91[ASN][1000 genomes]
rs7167760	0.94[CHB][hapmap]
rs7168749	0.88[ASN][1000 genomes]
rs7170980	0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs7171884	0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs7183479	0.94[CHB][hapmap]
rs744039	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8023455	0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs8033234	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs8034197	0.90[ASN][1000 genomes]
rs8037167	0.83[CHB][hapmap]
rs8037340	0.90[ASN][1000 genomes]
rs8042840	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1456299	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974400-51983400	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:51974400-51990800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:51974400-52005200	Weak transcription	Brain Anterior Caudate	brain
5	chr15:51974600-51983000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:51974600-51983200	Weak transcription	K562	blood
7	chr15:51974600-51984200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:51974600-51991000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:51974800-51984600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:51975000-51982600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:51975000-51993200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:51975200-51998400	Weak transcription	Brain Angular Gyrus	brain
14	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
15	chr15:51976800-51983200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:51978600-51990600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:51978800-51982200	Weak transcription	Fetal Brain Female	brain
18	chr15:51979800-51984400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:51980200-51988000	Strong transcription	Brain Germinal Matrix	brain
20	chr15:51981200-51983800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:51982000-51982200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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