Variant report

Variant	rs7597939
Chromosome Location	chr2:39814690-39814691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11680972	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11686518	0.89[AMR][1000 genomes]
rs13031765	0.84[EUR][1000 genomes]
rs34677610	0.86[EUR][1000 genomes]
rs4992380	0.88[EUR][1000 genomes]
rs6544235	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6722571	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7605812	0.88[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	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv961312	chr2:39810592-39817719	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7597939	MAP4K3	cis	cerebellum	SCAN
rs7597939	DHX57	cis	parietal	SCAN
rs7597939	CDC42EP3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39799600-39820800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:39808400-39815200	Weak transcription	HepG2	liver
3	chr2:39808400-39819000	Weak transcription	Liver	Liver
4	chr2:39809400-39821000	Weak transcription	Psoas Muscle	Psoas
5	chr2:39811200-39820600	Weak transcription	Left Ventricle	heart
6	chr2:39811600-39821000	Weak transcription	Brain Angular Gyrus	brain
7	chr2:39811800-39820800	Weak transcription	Brain Anterior Caudate	brain
8	chr2:39812000-39821000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:39812200-39821200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:39812400-39815000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:39812400-39815200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:39812400-39817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:39812400-39822400	Weak transcription	HSMM	muscle
14	chr2:39812600-39820800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:39812800-39815200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:39813000-39820800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:39814200-39820800	Weak transcription	Brain Inferior Temporal Lobe	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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