Variant report

Variant	rs1584402
Chromosome Location	chr2:116247080-116247081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10189544	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1026097	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1154727	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11694627	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12373737	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12711826	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13001120	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1402447	0.86[AFR][1000 genomes]
rs1448460	0.97[AFR][1000 genomes]
rs1521073	0.83[AFR][1000 genomes]
rs1550987	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1607913	0.82[AFR][1000 genomes]
rs1711999	0.83[AFR][1000 genomes]
rs1712001	0.97[AFR][1000 genomes]
rs1712003	0.82[AFR][1000 genomes]
rs1712013	0.82[AFR][1000 genomes]
rs1839134	0.97[AFR][1000 genomes]
rs1900747	0.97[AFR][1000 genomes]
rs2594828	0.90[AFR][1000 genomes]
rs4849405	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59033152	1.00[AMR][1000 genomes]
rs72945935	1.00[AMR][1000 genomes]
rs72945949	1.00[AMR][1000 genomes]
rs72945973	1.00[AMR][1000 genomes]
rs72945985	1.00[AMR][1000 genomes]
rs72945987	1.00[AMR][1000 genomes]
rs72947986	1.00[AMR][1000 genomes]
rs72947993	1.00[AMR][1000 genomes]
rs72947996	1.00[AMR][1000 genomes]
rs72961549	1.00[AMR][1000 genomes]
rs7575073	0.80[AFR][1000 genomes]
rs843380	0.83[AFR][1000 genomes]
rs843386	0.83[AFR][1000 genomes]
rs843387	0.83[AFR][1000 genomes]
rs843389	0.83[AFR][1000 genomes]
rs843400	0.86[AFR][1000 genomes]
rs843410	0.86[AFR][1000 genomes]
rs843431	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs843438	0.81[AFR][1000 genomes]
rs843439	0.93[AFR][1000 genomes]
rs843440	0.93[AFR][1000 genomes]
rs844541	0.86[AFR][1000 genomes]
rs861492	0.86[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014859	chr2:116196951-116938584	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1584402	TK2	trans	lymphoblastoid	seeQTL
rs1584402	SESTD1	trans	lymphoblastoid	seeQTL
rs1584402	CKLF	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:116237600-116249200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:116246600-116247200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:116246600-116247600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:116246600-116247600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:116246600-116247800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:116246600-116249000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:116246800-116247200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:116246800-116247600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:116246800-116247600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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