Variant report

Variant	rs154024
Chromosome Location	chr5:58636116-58636117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs154031	0.93[EUR][1000 genomes]
rs244573	0.97[EUR][1000 genomes]
rs244575	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs244577	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs35258	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs35261	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs35267	0.92[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs35276	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs35278	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs35279	0.92[EUR][1000 genomes]
rs35283	0.92[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs35284	0.92[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs39672	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs40122	0.92[CEU][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs154024	DDX3Y	trans	lymphoblastoid	seeQTL
rs154024	RAB3C	cis	parietal	SCAN
rs154024	RPS4Y1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58625000-58644600	Weak transcription	Left Ventricle	heart
2	chr5:58627400-58641600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58634400-58636800	Weak transcription	Psoas Muscle	Psoas
4	chr5:58634400-58647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:58635200-58640200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:58635200-58652600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:58635600-58637400	Weak transcription	Fetal Brain Male	brain
8	chr5:58635800-58636800	Weak transcription	A549	lung
9	chr5:58636000-58637400	Weak transcription	Fetal Heart	heart

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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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