Variant report

Variant	rs3770016
Chromosome Location	chr2:178540293-178540294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178128784..178131655-chr2:178537635..178541213,3	K562	blood:

Variant related genes	Relation type
ENSG00000116044	Chromatin interaction
ENSG00000222043	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10803913	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803914	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12475250	0.80[EUR][1000 genomes]
rs2886423	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770015	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433690	0.88[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv275124	chr2:178538584-178541159	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770016	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178535000-178544800	Weak transcription	Right Atrium	heart
2	chr2:178536000-178544600	Weak transcription	Psoas Muscle	Psoas
3	chr2:178536600-178540400	Weak transcription	Fetal Stomach	stomach
4	chr2:178536600-178556000	Weak transcription	Pancreas	Pancrea
5	chr2:178539800-178541800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:178540000-178540400	Active TSS	Brain Angular Gyrus	brain
7	chr2:178540000-178540400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr2:178540000-178540600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:178540000-178540600	Enhancers	Liver	Liver
10	chr2:178540000-178540600	Active TSS	Brain Anterior Caudate	brain
11	chr2:178540000-178540600	Active TSS	Brain Cingulate Gyrus	brain
12	chr2:178540000-178540600	Enhancers	Fetal Lung	lung
13	chr2:178540000-178540600	Enhancers	Fetal Muscle Leg	muscle
14	chr2:178540000-178541400	Enhancers	Colon Smooth Muscle	Colon
15	chr2:178540000-178541400	Enhancers	Ovary	ovary
16	chr2:178540000-178541400	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:178540000-178547400	Enhancers	Fetal Kidney	kidney
18	chr2:178540200-178540400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:178540200-178540600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:178540200-178540600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:178540200-178540600	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr2:178540200-178540600	Active TSS	Brain Substantia Nigra	brain
23	chr2:178540200-178540600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr2:178540200-178540800	Enhancers	Brain Germinal Matrix	brain
25	chr2:178540200-178541400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:178540200-178544600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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