Variant report

Variant	rs12575115
Chromosome Location	chr11:18794370-18794371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs35763160	0.80[ASN][1000 genomes]
rs4073915	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265582	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268487	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56295396	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121896	0.86[ASN][1000 genomes]
rs7129580	0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12575115	PTPN5	cis	Stomach	GTEx
rs12575115	PTPN5	cis	Nerve Tibial	GTEx

Chromatin state (count:17 , 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	chr11:18790800-18795000	Weak transcription	Brain Anterior Caudate	brain
4	chr11:18790800-18811400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:18793000-18794600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr11:18793400-18794800	Enhancers	Fetal Brain Male	brain
7	chr11:18793600-18809000	Weak transcription	Brain Angular Gyrus	brain
8	chr11:18793800-18795200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:18793800-18796000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr11:18794000-18794400	Enhancers	HSMMtube	muscle
11	chr11:18794000-18795400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr11:18794000-18795400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:18794000-18795600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:18794000-18796200	Enhancers	Fetal Muscle Trunk	muscle
15	chr11:18794200-18795400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr11:18794200-18795600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr11:18794200-18795600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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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

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