Variant report

Variant	rs1996893
Chromosome Location	chr9:14890268-14890269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10810278	0.81[CEU][hapmap]
rs10810283	0.81[CEU][hapmap]
rs1889048	0.81[CEU][hapmap]
rs1889049	0.81[CEU][hapmap]
rs1889051	0.81[CEU][hapmap]
rs1889052	0.81[CEU][hapmap]
rs6474862	0.81[CEU][hapmap]
rs6474863	0.81[CEU][hapmap]
rs6474865	0.81[CEU][hapmap]
rs7019358	0.81[CEU][hapmap]
rs7020282	0.81[CEU][hapmap]
rs7048511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7867761	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	esv3390567	chr9:14852461-14891880	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1996893	FREM1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14881200-14904600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:14882000-14899000	Weak transcription	Pancreas	Pancrea
3	chr9:14882000-14902400	Weak transcription	Fetal Stomach	stomach
4	chr9:14884200-14907400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:14884400-14899200	Weak transcription	Aorta	Aorta
6	chr9:14887400-14899200	Weak transcription	Adipose Nuclei	Adipose
7	chr9:14887400-14902200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:14887600-14891200	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:14889000-14890400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:14889000-14890400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr9:14889400-14891400	Weak transcription	HepG2	liver
12	chr9:14889800-14890400	Genic enhancers	Fetal Lung	lung
13	chr9:14889800-14891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:14889800-14900000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:14890200-14892000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:14890200-14892800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:14890200-14899200	Weak transcription	Fetal Kidney	kidney

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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