Variant report

Variant	rs38117
Chromosome Location	chr7:78256643-78256644
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs161285	0.90[ASN][1000 genomes]
rs191181	0.90[ASN][1000 genomes]
rs319863	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs321975	0.80[JPT][hapmap]
rs38096	0.90[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs38098	0.90[GIH][hapmap]
rs38099	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs38100	0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38102	0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38103	0.85[GIH][hapmap]
rs38104	0.85[GIH][hapmap]
rs38105	0.92[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38107	0.85[GIH][hapmap]
rs38108	0.91[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38109	0.95[GIH][hapmap]
rs38111	0.91[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38113	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38115	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38119	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs38117	PTPN12	cis	cerebellum	SCAN
rs38117	YWHAG	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78219000-78258600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:78252400-78256800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:78252600-78266400	Weak transcription	Aorta	Aorta
4	chr7:78254200-78256800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:78254200-78268800	Weak transcription	Brain Germinal Matrix	brain
6	chr7:78255200-78256800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:78255800-78257800	Enhancers	Brain Angular Gyrus	brain
8	chr7:78255800-78258600	Enhancers	Brain Cingulate Gyrus	brain
9	chr7:78256200-78257600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr7:78256400-78257000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr7:78256400-78257400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:78256400-78257600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:78256400-78257600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:78256400-78257800	Enhancers	Brain Substantia Nigra	brain
15	chr7:78256400-78258600	Enhancers	Brain Anterior Caudate	brain
16	chr7:78256400-78258800	Enhancers	Brain Hippocampus Middle	brain
17	chr7:78256600-78257000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr7:78256600-78257000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:78256600-78257400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:78256600-78257600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr7:78256600-78257600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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