Variant report

Variant	rs10122340
Chromosome Location	chr9:14911241-14911242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10756626	0.83[GIH][hapmap]
rs1855142	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs1916314	1.00[CEU][hapmap];0.87[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2030594	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2140323	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3850442	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3922832	0.87[GIH][hapmap]
rs6474871	0.99[ASN][1000 genomes]
rs6474872	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7848497	0.93[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.85[AMR][1000 genomes]
rs7861117	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7865084	0.85[AMR][1000 genomes]
rs940119	0.81[AMR][1000 genomes]
rs940120	0.91[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831518	chr9:14760638-14953501	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1018416	chr9:14846753-14921247	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10122340	FREM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14907400-14915000	Weak transcription	Small Intestine	intestine
2	chr9:14910400-14921000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:14910800-14911400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:14910800-14911400	Enhancers	Colon Smooth Muscle	Colon
5	chr9:14910800-14911400	Enhancers	Fetal Stomach	stomach
6	chr9:14910800-14911400	Enhancers	HepG2	liver
7	chr9:14910800-14911600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:14910800-14911600	Enhancers	Fetal Brain Male	brain
9	chr9:14910800-14911600	Enhancers	Rectal Smooth Muscle	rectum
10	chr9:14910800-14913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:14910800-14915800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:14911000-14911400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:14911000-14912800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:14911000-14913400	Enhancers	Fetal Lung	lung
15	chr9:14911200-14912600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:14911200-14912600	Weak transcription	Fetal Heart	heart
17	chr9:14911200-14912800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:14911200-14913200	Enhancers	Fetal Kidney	kidney

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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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