Variant report

Variant	rs4541508
Chromosome Location	chr4:110682487-110682488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10016598	0.82[ASN][1000 genomes]
rs10049804	0.84[ASN][1000 genomes]
rs10857001	0.84[ASN][1000 genomes]
rs11721403	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11734208	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11943677	0.81[ASN][1000 genomes]
rs13129180	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs3188897	0.83[ASW][hapmap]
rs4469075	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4698784	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs6533457	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841303	0.81[ASN][1000 genomes]
rs7438961	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[ASN][1000 genomes]
rs7439356	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7440009	0.81[ASN][1000 genomes]
rs7675460	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9654197	0.82[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	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv4463	chr4:110647731-110693125	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4541508	LRIT3	cis	cerebellum	SCAN
rs4541508	RRH	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110652000-110682800	Weak transcription	Left Ventricle	heart
2	chr4:110652000-110686000	Weak transcription	Ovary	ovary
3	chr4:110658000-110684000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:110659200-110689000	Weak transcription	Fetal Intestine Large	intestine
5	chr4:110665000-110690400	Weak transcription	Fetal Intestine Small	intestine
6	chr4:110670600-110692000	Weak transcription	Pancreas	Pancrea
7	chr4:110676600-110684200	Strong transcription	Liver	Liver
8	chr4:110681000-110683000	Strong transcription	HepG2	liver
9	chr4:110682000-110683200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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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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