Variant report

Variant	rs12236086
Chromosome Location	chr9:8862724-8862725
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr9:8862492-8862809	A549	lung:	n/a	chr9:8862647-8862660 chr9:8862648-8862659 chr9:8862649-8862658 chr9:8862647-8862658 chr9:8862647-8862660
2	CEBPB	chr9:8862489-8862789	H1-hESC	embryonic stem cell:	n/a	chr9:8862647-8862660 chr9:8862648-8862659 chr9:8862649-8862658 chr9:8862647-8862658 chr9:8862647-8862660
3	CEBPB	chr9:8862470-8862814	HepG2	liver:	n/a	chr9:8862647-8862660 chr9:8862648-8862659 chr9:8862649-8862658 chr9:8862647-8862658 chr9:8862647-8862660
4	CEBPB	chr9:8862468-8862816	IMR90	lung:	n/a	chr9:8862647-8862660 chr9:8862648-8862659 chr9:8862649-8862658 chr9:8862647-8862658 chr9:8862647-8862660

Variant related genes	Relation type
PTPRD	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10759007	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10815979	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs10977326	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10977327	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs1368686	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs1991863	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147225	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12236086	PDCD1LG2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8858800-8871400	Enhancers	Fetal Heart	heart
2	chr9:8859000-8864200	Weak transcription	Aorta	Aorta
3	chr9:8859200-8863000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:8859200-8863800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:8859200-8864000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:8859400-8864000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:8859400-8864000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:8859400-8864000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:8859400-8870800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:8859600-8866400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:8859800-8863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:8860200-8864400	Weak transcription	Ovary	ovary
13	chr9:8860200-8864600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:8860200-8867400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:8860400-8863000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:8860400-8863800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:8860400-8864200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:8860600-8863800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:8860800-8867200	Weak transcription	Brain Germinal Matrix	brain
20	chr9:8861000-8863000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:8861000-8863000	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:8861000-8864200	Weak transcription	Brain Anterior Caudate	brain
23	chr9:8861200-8863000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:8861200-8863200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:8861200-8864200	Weak transcription	Brain Angular Gyrus	brain
26	chr9:8861200-8867400	Weak transcription	Fetal Brain Female	brain
27	chr9:8861400-8863200	Weak transcription	NH-A	brain
28	chr9:8862400-8863600	Enhancers	Brain Substantia Nigra	brain
29	chr9:8862600-8863200	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:8862600-8863400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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