Variant report

Variant	rs2459396
Chromosome Location	chr15:51688996-51688997
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11070857	0.81[CHB][hapmap]
rs12438892	0.81[CHB][hapmap]
rs2124875	0.81[CHB][hapmap]
rs2445746	0.86[YRI][hapmap]
rs2445747	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2445748	0.95[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2445749	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2445750	0.85[CEU][hapmap]
rs2459395	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs898134	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	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
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2459396	DMXL2	cis	parietal	SCAN
rs2459396	DMXL2	cis	cerebellum	SCAN
rs2459396	SQRDL	cis	cerebellum	SCAN
rs2459396	KIAA1370	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51672600-51691000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:51673600-51694000	Weak transcription	Spleen	Spleen
3	chr15:51677600-51690800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:51678200-51697800	Weak transcription	Brain Anterior Caudate	brain
5	chr15:51679800-51693000	Weak transcription	Brain Substantia Nigra	brain
6	chr15:51682000-51691600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:51686400-51690800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:51686400-51694000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:51687000-51689800	Strong transcription	Aorta	Aorta
10	chr15:51687200-51700400	Strong transcription	Placenta	Placenta
11	chr15:51688200-51689000	Genic enhancers	Brain Hippocampus Middle	brain
12	chr15:51688400-51689200	Enhancers	Brain Angular Gyrus	brain
13	chr15:51688600-51693000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr15:51688600-51693200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:51688800-51689000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:51688800-51689000	Enhancers	Brain Germinal Matrix	brain
17	chr15:51688800-51689600	Strong transcription	Adipose Nuclei	Adipose
18	chr15:51688800-51708600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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