Variant report

Variant	rs2189553
Chromosome Location	chrY:16826711-16826712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10245408	0.82[ASN][1000 genomes]
rs10260325	0.83[ASN][1000 genomes]
rs10260826	0.82[ASN][1000 genomes]
rs10435042	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10464197	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464265	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464266	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464267	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10464268	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464269	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10486121	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10486124	0.84[ASN][1000 genomes]
rs1120296	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1574878	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17164220	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17164261	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17164306	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4719262	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4719263	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4719264	0.81[ASN][1000 genomes]
rs4720961	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4720962	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4720963	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4720964	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4720966	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5006296	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5021557	0.80[ASN][1000 genomes]
rs72586111	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72586113	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72586128	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72586130	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72586131	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72586135	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72586138	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72586139	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72586144	0.84[ASN][1000 genomes]
rs72586148	0.83[ASN][1000 genomes]
rs72586150	0.83[ASN][1000 genomes]
rs739893	0.83[ASN][1000 genomes]
rs763502	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs763654	0.83[ASN][1000 genomes]

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	esv3409548	chrY:16169870-17053457	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv869394	chrY:16699218-17364088	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrY:16799600-16842200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chrY:16808200-16850800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chrY:16813800-16835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chrY:16821000-16827600	Weak transcription	HUVEC	blood vessel
5	chrY:16822800-16845600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chrY:16823000-16852000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chrY:16824600-16845600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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