Variant report

Variant	rs2938109
Chromosome Location	chr7:25589591-25589592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1393672	0.88[EUR][1000 genomes]
rs289997	0.84[EUR][1000 genomes]
rs2938108	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2960816	0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999569	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73277029	0.82[EUR][1000 genomes]
rs905385	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs965610	0.81[AFR][1000 genomes]
rs981903	0.84[AFR][1000 genomes];0.87[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	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25579800-25600800	Weak transcription	Lung	lung
2	chr7:25585600-25593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:25587800-25589600	Enhancers	Fetal Lung	lung
4	chr7:25588000-25593000	Weak transcription	Fetal Brain Male	brain
5	chr7:25588200-25589800	Enhancers	Ovary	ovary
6	chr7:25588400-25590200	Enhancers	Fetal Stomach	stomach
7	chr7:25589000-25589600	Enhancers	Fetal Kidney	kidney
8	chr7:25589000-25589600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr7:25589000-25589800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:25589200-25590600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:25589200-25593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:25589400-25589800	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr7:25589400-25593400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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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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