Variant report

Variant	rs10815977
Chromosome Location	chr9:8860355-8860356
allele	A/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	ZNF263	chr9:8856641-8860520	HEK293-T-REx	kidney:	n/a	chr9:8858101-8858122 chr9:8859812-8859821 chr9:8858020-8858029

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-8	chr9:8859956-8861724	ENSG00000225706

Variant related genes	Relation type
PTPRD	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10759007	0.80[AMR][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
rs10815977	PDCD1LG2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8858800-8871400	Enhancers	Fetal Heart	heart
2	chr9:8859000-8860400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr9:8859000-8864200	Weak transcription	Aorta	Aorta
4	chr9:8859200-8860400	Enhancers	Fetal Muscle Leg	muscle
5	chr9:8859200-8861200	Enhancers	Fetal Stomach	stomach
6	chr9:8859200-8863000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:8859200-8863800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:8859200-8864000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:8859400-8860400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:8859400-8860600	Enhancers	Fetal Kidney	kidney
11	chr9:8859400-8860800	Enhancers	Brain Germinal Matrix	brain
12	chr9:8859400-8861000	Enhancers	Brain Substantia Nigra	brain
13	chr9:8859400-8861200	Enhancers	Brain Angular Gyrus	brain
14	chr9:8859400-8864000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:8859400-8864000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:8859400-8864000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:8859400-8870800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:8859600-8860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:8859600-8860400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:8859600-8861000	Enhancers	Fetal Brain Male	brain
21	chr9:8859600-8861000	Bivalent Enhancer	Fetal Lung	lung
22	chr9:8859600-8862600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:8859600-8866400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:8859800-8861200	Enhancers	Fetal Brain Female	brain
25	chr9:8859800-8861400	Enhancers	Brain Hippocampus Middle	brain
26	chr9:8859800-8863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:8860000-8861000	Enhancers	Brain Anterior Caudate	brain
28	chr9:8860000-8861200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:8860200-8860400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:8860200-8861200	Enhancers	Brain Cingulate Gyrus	brain
31	chr9:8860200-8864400	Weak transcription	Ovary	ovary
32	chr9:8860200-8864600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:8860200-8867400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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