Variant report

Variant	rs1426028
Chromosome Location	chr3:139727563-139727564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12491613	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1426027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426034	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16849630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16849640	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16849687	0.92[JPT][hapmap]
rs16849696	0.84[JPT][hapmap]
rs16849705	0.92[JPT][hapmap]
rs16849709	0.92[JPT][hapmap]
rs16849713	0.92[JPT][hapmap]
rs16849718	0.92[JPT][hapmap]
rs16849742	0.92[JPT][hapmap]
rs4683473	0.88[JPT][hapmap]
rs4683474	0.92[JPT][hapmap]
rs4683774	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683786	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683792	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1426028	SLC25A36	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139714400-139741200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:139722200-139733400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:139724000-139727800	Enhancers	Fetal Muscle Leg	muscle
4	chr3:139725200-139728000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:139725400-139728000	Enhancers	Brain Germinal Matrix	brain
6	chr3:139725600-139731000	Weak transcription	Fetal Brain Male	brain
7	chr3:139726200-139727600	Enhancers	Fetal Muscle Trunk	muscle
8	chr3:139726200-139727800	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:139726800-139727600	Enhancers	Ovary	ovary
10	chr3:139726800-139728200	Enhancers	Brain Hippocampus Middle	brain
11	chr3:139726800-139731400	Weak transcription	HSMMtube	muscle
12	chr3:139727000-139727600	Enhancers	Fetal Brain Female	brain
13	chr3:139727000-139727800	Enhancers	Brain Angular Gyrus	brain
14	chr3:139727000-139727800	Enhancers	Brain Substantia Nigra	brain
15	chr3:139727200-139727600	Enhancers	Psoas Muscle	Psoas
16	chr3:139727200-139727800	Enhancers	Brain Anterior Caudate	brain
17	chr3:139727200-139727800	Enhancers	Pancreas	Pancrea
18	chr3:139727200-139728400	Enhancers	Liver	Liver

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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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