Variant report

Variant	rs1578900
Chromosome Location	chr5:164658422-164658423
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10064661	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10067676	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10076780	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10076821	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10866752	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11747004	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11747437	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11747503	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11748440	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11748996	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11749187	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12519113	0.97[ASN][1000 genomes]
rs12519127	0.96[ASN][1000 genomes]
rs13186057	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17333449	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17391889	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35203349	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35665300	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4130573	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130574	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291037	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4367315	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4868753	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4868918	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4868919	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4868920	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62385686	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7700285	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7715290	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7720784	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7731911	0.89[AMR][1000 genomes];0.94[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	nsv528624	chr5:164319435-164701201	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1033866	chr5:164419608-164677758	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1027138	chr5:164563093-164852655	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537937	chr5:164563093-164852655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1028006	chr5:164563293-164852516	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv537938	chr5:164563293-164852516	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1027103	chr5:164606534-164694498	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1578900	FLT3	trans	cerebellum	SCAN
rs1578900	GOT1L1	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:164656600-164658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:164656600-164658600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:164656600-164658800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:164657400-164659200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:164657800-164659400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:164657800-164660200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:164657800-164660600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:164657800-164660600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:164657800-164660800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr5:164658200-164659200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:164658200-164659400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr5:164658200-164659400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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