Variant report

Variant	rs1880212
Chromosome Location	chr3:61233908-61233909
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17064638	0.84[CHD][hapmap]
rs2365491	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365492	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28670997	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55699767	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56268052	0.83[AMR][1000 genomes]
rs6772523	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap]
rs6777895	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73098964	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098998	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880212	PTPRG	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61224000-61235200	Weak transcription	K562	blood
2	chr3:61224800-61234400	Weak transcription	GM12878-XiMat	blood
3	chr3:61226200-61235600	Weak transcription	Left Ventricle	heart
4	chr3:61226200-61235600	Weak transcription	Right Atrium	heart
5	chr3:61226200-61235800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:61227000-61235600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:61227000-61235600	Weak transcription	Pancreas	Pancrea
8	chr3:61228200-61235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:61228800-61235400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:61228800-61235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:61229000-61236000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:61229000-61236000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:61230600-61235400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:61230600-61236800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:61230800-61235400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:61230800-61235800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:61231000-61235600	Weak transcription	Fetal Heart	heart
18	chr3:61231800-61235800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:61232800-61234000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:61232800-61234200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:61232800-61234600	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:61232800-61234600	Enhancers	Brain Substantia Nigra	brain
23	chr3:61232800-61234600	Enhancers	Ovary	ovary
24	chr3:61232800-61234800	Enhancers	Brain Hippocampus Middle	brain
25	chr3:61233000-61235600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:61233200-61235800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:61233200-61236000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:61233200-61236000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:61233200-61236600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:61233200-61236600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:61233400-61234800	Enhancers	Brain Angular Gyrus	brain
32	chr3:61233400-61235400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:61233800-61234200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:61233800-61234600	Enhancers	Brain Anterior Caudate	brain

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