Variant report

Variant	rs4265582
Chromosome Location	chr11:18797650-18797651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12575115	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35763160	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4073915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075663	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs56268487	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56295396	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121896	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7129580	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv525452	chr11:18735947-18802503	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4265582	PTPN5	cis	Nerve Tibial	GTEx
rs4265582	HINFP	trans	brain	seeQTL
rs4265582	RBM10	trans	brain	seeQTL
rs4265582	SEMA3G	trans	brain	seeQTL
rs4265582	PTPN5	cis	Stomach	GTEx
rs4265582	PTPN5	cis	Esophagus Muscularis	GTEx
rs4265582	MYOD1	cis	parietal	SCAN
rs4265582	SPEG	trans	brain	seeQTL
rs4265582	CA4	trans	brain	seeQTL
rs4265582	PER3	trans	brain	seeQTL
rs4265582	CNNM3	trans	brain	seeQTL
rs4265582	PTPN5	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18783000-18801800	Weak transcription	Spleen	Spleen
2	chr11:18784000-18808000	Weak transcription	Fetal Brain Female	brain
3	chr11:18790800-18811400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:18793600-18809000	Weak transcription	Brain Angular Gyrus	brain
5	chr11:18794600-18811800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:18795200-18801400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:18795400-18801400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:18795400-18804600	Weak transcription	Brain Anterior Caudate	brain
9	chr11:18796000-18800400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:18796000-18800600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:18796000-18802000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:18796400-18812400	Weak transcription	Right Atrium	heart
13	chr11:18797400-18797800	Enhancers	Pancreas	Pancrea

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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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