Variant report

Variant	rs1554861
Chromosome Location	chr8:35124178-35124179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11781624	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12216854	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13256407	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1534583	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1534586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554862	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1590094	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1590095	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1819086	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1919335	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1919342	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1919343	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1919351	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1919353	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1969543	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2037839	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2056768	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2091566	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2141433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2178254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2178257	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950902	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950906	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950907	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950908	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950911	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950912	0.86[EUR][1000 genomes]
rs2950913	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950914	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950923	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950926	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2950932	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980381	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980382	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980383	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980384	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980385	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980393	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980394	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980395	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2980396	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2980401	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2980402	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108616	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108621	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108626	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4582555	0.85[EUR][1000 genomes]
rs4739301	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6468312	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6468314	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6996861	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7003669	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7830166	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7832774	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[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	nsv1017085	chr8:34742896-35594241	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539546	chr8:34742896-35594241	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831284	chr8:35018419-35193084	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv429910	chr8:35021411-35257445	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1554861	LETM2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35096000-35135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:35116200-35139200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:35118200-35133800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:35123400-35124600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr8:35123600-35124600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr8:35123800-35124400	ZNF genes & repeats	Fetal Brain Female	brain
7	chr8:35123800-35124600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr8:35123800-35124600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr8:35123800-35124600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
10	chr8:35123800-35124600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:35123800-35124600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr8:35124000-35124400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr8:35124000-35124400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr8:35124000-35124400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:35124000-35124400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:35124000-35124800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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