Variant report

Variant	rs2594731
Chromosome Location	chr3:118963980-118963981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10934486	0.87[CEU][hapmap]
rs12487052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12492305	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13315549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13320556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs13324867	1.00[CEU][hapmap]
rs16829413	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs28428903	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4234656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4450805	0.87[CEU][hapmap]
rs6438510	1.00[YRI][hapmap]
rs6766503	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6774	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6805930	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9840064	0.86[MEX][hapmap];0.87[TSI][hapmap]
rs9844248	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2594731	GOLGB1	cis	parietal	SCAN
rs2594731	PTPLB	cis	cerebellum	SCAN
rs2594731	C3orf30	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118960000-118964400	Weak transcription	Esophagus	oesophagus
2	chr3:118960200-118964200	Weak transcription	Psoas Muscle	Psoas
3	chr3:118960200-118964600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:118960200-118964600	Weak transcription	Right Atrium	heart
5	chr3:118960200-118964800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:118960400-118964400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:118960400-118966200	Weak transcription	Primary T cells from cord blood	blood
8	chr3:118960600-118964400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:118960600-118964600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:118960600-118964800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:118960600-118964800	Weak transcription	Placenta	Placenta
12	chr3:118960800-118964600	Weak transcription	Stomach Mucosa	stomach
13	chr3:118961000-118964600	Weak transcription	Right Ventricle	heart
14	chr3:118961600-118967400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:118962800-118966000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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