Variant report

Variant	rs7928480
Chromosome Location	chr11:45407494-45407495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10838464	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838465	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838467	0.84[EUR][1000 genomes]
rs11038428	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12224037	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12271560	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12275086	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs1873056	0.84[EUR][1000 genomes]
rs2046733	0.84[EUR][1000 genomes]
rs34042421	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35072015	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59678781	0.84[EUR][1000 genomes]
rs7943688	0.84[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	nsv530619	chr11:45294176-45553928	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv467869	chr11:45389225-45415035	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv554185	chr11:45389225-45415035	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7928480	MTCH2	cis	parietal	SCAN
rs7928480	LRP4	cis	parietal	SCAN
rs7928480	SYT13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45403200-45408400	Enhancers	Brain Germinal Matrix	brain
2	chr11:45403200-45410000	Enhancers	Fetal Thymus	thymus
3	chr11:45403600-45407800	Enhancers	Thymus	Thymus
4	chr11:45403600-45408000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr11:45404200-45407800	Enhancers	Fetal Brain Male	brain
6	chr11:45404800-45407600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr11:45405400-45434800	Weak transcription	Right Atrium	heart
8	chr11:45406000-45408800	Enhancers	Fetal Brain Female	brain
9	chr11:45406000-45409200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:45406200-45408600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:45406400-45407600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:45406400-45407600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:45406400-45407600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr11:45406400-45407800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:45406600-45407600	Bivalent Enhancer	Primary T cells from cord blood	blood
16	chr11:45407000-45407600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:45407000-45421000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:45407200-45407600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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