Variant report

Variant	rs1990712
Chromosome Location	chr7:108024132-108024133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12531089	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs12539530	0.85[CEU][hapmap]
rs12539964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13230316	0.81[EUR][1000 genomes]
rs13244715	0.83[EUR][1000 genomes]
rs2080489	0.80[EUR][1000 genomes]
rs2216259	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2284286	0.83[EUR][1000 genomes]
rs2284287	0.81[EUR][1000 genomes]
rs2284288	0.83[EUR][1000 genomes]
rs2300027	0.85[CEU][hapmap]
rs2395961	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2395962	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35669142	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36063908	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56102707	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6975557	0.85[CEU][hapmap]
rs7804045	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1990712	NRCAM	cis	cerebellum	SCAN
rs1990712	LRRN3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:108020000-108034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:108021400-108040800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:108021400-108043000	Weak transcription	HMEC	breast
5	chr7:108021800-108025000	Weak transcription	A549	lung
6	chr7:108021800-108026600	Weak transcription	HUVEC	blood vessel
7	chr7:108022400-108034200	Weak transcription	Pancreas	Pancrea
8	chr7:108023200-108024400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr7:108023600-108024400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:108023800-108024200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:108023800-108024400	Enhancers	Brain Angular Gyrus	brain
12	chr7:108023800-108024400	Active TSS	Fetal Brain Male	brain
13	chr7:108024000-108025400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:108024000-108033000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:108024000-108045600	Weak transcription	Brain Anterior Caudate	brain

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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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