Variant report

Variant	rs17648128
Chromosome Location	chr15:51689772-51689773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12592390	0.82[CHB][hapmap]
rs12592422	0.82[CHB][hapmap]
rs17648104	0.84[CEU][hapmap]
rs17648140	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1914020	0.83[ASN][1000 genomes]
rs2445746	0.86[CHB][hapmap]
rs2445751	0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2470192	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2470194	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4774590	0.81[CEU][hapmap]
rs4775945	0.82[CHB][hapmap]
rs62018073	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493498	0.86[CHB][hapmap]
rs8034340	0.82[CHB][hapmap]
rs898134	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs898135	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs930919	0.81[CHB][hapmap]
rs9744072	0.87[EUR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17648128	LYSMD2	cis	parietal	SCAN
rs17648128	ATP8B4	cis	cerebellum	SCAN
rs17648128	DMXL2	Cis_1M	lymphoblastoid	RTeQTL
rs17648128	SCG3	cis	cerebellum	SCAN
rs17648128	SHF	cis	parietal	SCAN
rs17648128	ARPP19	cis	parietal	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	chr15:51688600-51693000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:51688600-51693200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:51688800-51708600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:51689000-51690600	Weak transcription	Brain Germinal Matrix	brain
15	chr15:51689200-51690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:51689200-51692800	Weak transcription	Brain Angular Gyrus	brain
17	chr15:51689400-51690800	Strong transcription	Brain Hippocampus Middle	brain
18	chr15:51689600-51707000	Weak transcription	Adipose Nuclei	Adipose

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Input of quick search could be:

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

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