Variant report

Variant	rs38102
Chromosome Location	chr7:78242804-78242805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs161285	0.89[ASN][1000 genomes]
rs191181	0.89[ASN][1000 genomes]
rs319863	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs321975	0.81[JPT][hapmap]
rs38096	0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs38098	0.86[GIH][hapmap]
rs38099	0.82[EUR][1000 genomes]
rs38100	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38103	0.81[CEU][hapmap];1.00[GIH][hapmap]
rs38104	0.80[CEU][hapmap];1.00[GIH][hapmap]
rs38105	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38107	0.81[CEU][hapmap];1.00[GIH][hapmap]
rs38108	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38109	0.90[GIH][hapmap]
rs38111	0.83[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38113	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38115	0.84[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38117	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]
rs38119	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38102	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

Quick Search:

Input of quick search could be:

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

what's new

Quick links