Variant report

Variant	rs11984041
Chromosome Location	chr7:19031935-19031936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10241964	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10245779	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10255384	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2023937	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2023938	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526619	0.83[EUR][1000 genomes]
rs2717334	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28727433	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59111453	0.92[AMR][1000 genomes]
rs7783974	0.92[AMR][1000 genomes]
rs7784712	0.84[AMR][1000 genomes]
rs7792656	0.89[AMR][1000 genomes];0.84[EUR][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	nsv531020	chr7:18971153-19261019	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv887817	chr7:19021592-19100076	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Stroke	22306652	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11984041	TOMM7	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19013800-19040800	Weak transcription	Aorta	Aorta
2	chr7:19015800-19042400	Weak transcription	Left Ventricle	heart
3	chr7:19018800-19033600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:19019400-19034600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:19030400-19034800	Weak transcription	Adipose Nuclei	Adipose
6	chr7:19030600-19035600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:19030600-19035600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:19030800-19032000	Strong transcription	NHDF-Ad	bronchial
9	chr7:19031600-19032000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:19031600-19032200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr7:19031800-19035600	Weak transcription	Brain Germinal Matrix	brain

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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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