Variant report

Variant	rs38104
Chromosome Location	chr7:78244685-78244686
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs161287	0.95[JPT][hapmap];0.84[MEX][hapmap]
rs161288	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs319861	0.83[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs319862	0.83[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs38096	0.82[GIH][hapmap]
rs38098	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs38100	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs38102	0.80[CEU][hapmap];1.00[GIH][hapmap]
rs38103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38105	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[GIH][hapmap];0.92[YRI][hapmap]
rs38107	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38108	0.96[YRI][hapmap]
rs38109	0.83[ASW][hapmap];0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38111	0.89[ASW][hapmap];0.95[GIH][hapmap];0.85[YRI][hapmap]
rs38113	0.80[AFR][1000 genomes]
rs38114	0.83[CEU][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs38117	0.85[GIH][hapmap]
rs38120	0.83[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][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
rs38104	PTPN12	cis	cerebellum	SCAN

Chromatin state (count:4 , 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	chr7:78236800-78256400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:78238400-78255800	Weak transcription	Brain Angular Gyrus	brain
4	chr7:78240400-78256400	Weak transcription	Fetal Brain Male	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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