Variant report

Variant	rs10814395
Chromosome Location	chr9:3660648-3660649
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1334063	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537523	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs1537524	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs1548299	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6476554	0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs7865839	0.87[ASN][1000 genomes]
rs7873232	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv892092	chr9:3565211-3687942	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1033417	chr9:3594189-3732530	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1021394	chr9:3594389-3728995	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1032487	chr9:3601907-3661151	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv892093	chr9:3613712-3696874	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
8	nsv892094	chr9:3631008-3783874	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv892095	chr9:3650174-3749196	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10814395	GLDC	cis	cerebellum	SCAN
rs10814395	UHRF2	cis	cerebellum	SCAN
rs10814395		cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3647800-3678200	Weak transcription	Psoas Muscle	Psoas
2	chr9:3656600-3663400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:3657200-3661200	Weak transcription	Pancreas	Pancrea
4	chr9:3658000-3673600	Weak transcription	Gastric	stomach
5	chr9:3659800-3661000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:3659800-3676200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:3660000-3660800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:3660000-3660800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:3660200-3661400	Enhancers	Fetal Lung	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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