Variant report

Variant	rs1540052
Chromosome Location	chr4:103137977-103137978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10002033	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943887	0.81[AFR][1000 genomes]
rs11943915	0.86[AFR][1000 genomes]
rs11943924	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs151413	0.86[AFR][1000 genomes]
rs151414	0.86[AFR][1000 genomes]
rs151416	0.86[AFR][1000 genomes]
rs151417	0.86[AFR][1000 genomes]
rs17032168	0.86[AFR][1000 genomes]
rs28855675	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62322244	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62322246	0.86[AFR][1000 genomes]
rs7662378	0.82[TSI][hapmap]
rs7674104	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7690879	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs978999	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv428447	chr4:103103730-103262107	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1540052	AIMP1	cis	cerebellum	SCAN
rs1540052	GSTCD	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103132400-103139200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:103137200-103139400	Enhancers	A549	lung
3	chr4:103137400-103138200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:103137600-103138000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr4:103137800-103138000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:103137800-103138000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr4:103137800-103138200	Weak transcription	Hela-S3	cervix
8	chr4:103137800-103139600	Weak transcription	ES-I3 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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