Variant report

Variant	rs7789112
Chromosome Location	chr7:78125648-78125649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs2110630	0.80[CHB][hapmap];1.00[YRI][hapmap]
rs2192648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2192649	0.87[AFR][1000 genomes]
rs35114939	0.86[AFR][1000 genomes]
rs4421288	0.87[AFR][1000 genomes]
rs4730332	0.86[AFR][1000 genomes]
rs4730343	0.87[YRI][hapmap]
rs4730345	0.87[YRI][hapmap]
rs6466258	0.87[YRI][hapmap]
rs7805441	0.91[ASW][hapmap];0.86[CHB][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7789112	PTPN12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78114800-78127800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:78119400-78125800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:78119400-78128000	Enhancers	Brain Substantia Nigra	brain
4	chr7:78119400-78130200	Weak transcription	Aorta	Aorta
5	chr7:78119600-78145600	Weak transcription	Ovary	ovary
6	chr7:78119800-78128400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:78119800-78132400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:78121800-78125800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:78122000-78127400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:78122000-78130400	Weak transcription	Brain Germinal Matrix	brain
11	chr7:78122400-78125800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:78122600-78143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:78123000-78125800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:78123000-78126600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:78124800-78126000	Active TSS	Brain Hippocampus Middle	brain
16	chr7:78125400-78125800	Active TSS	Brain Anterior Caudate	brain
17	chr7:78125400-78126000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:78125400-78126000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr7:78125400-78126000	Active TSS	Brain Cingulate Gyrus	brain
20	chr7:78125400-78126400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:78125400-78126400	Enhancers	Brain Angular Gyrus	brain
22	chr7:78125600-78125800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:78125600-78126200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:78125600-78126200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr7:78125600-78126200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr7:78125600-78128600	Enhancers	HUES48 Cell Line	embryonic stem cell

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