Variant report

Variant	rs12339993
Chromosome Location	chr9:13720823-13720824
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10115052	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10125903	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12344708	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12350251	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13292780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34324640	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs496857	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs504659	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs537556	0.85[EUR][1000 genomes]
rs594872	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs611973	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs612828	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs627216	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs629775	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs648981	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs789583	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs789593	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs789598	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv1023684	chr9:13529680-13744602	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv540067	chr9:13529680-13744602	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv892587	chr9:13601074-13732363	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1018933	chr9:13669862-13756710	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892590	chr9:13689066-13777299	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1022001	chr9:13717736-13983738	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13716800-13722000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:13717200-13721600	Enhancers	NH-A	brain
3	chr9:13717400-13721000	Enhancers	Osteobl	bone
4	chr9:13717400-13722200	Enhancers	HSMMtube	muscle
5	chr9:13717600-13728000	Weak transcription	HUVEC	blood vessel
6	chr9:13717800-13721200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:13718200-13727400	Weak transcription	Fetal Brain Male	brain
8	chr9:13718400-13721800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:13719400-13722000	Enhancers	NHDF-Ad	bronchial
10	chr9:13719800-13721600	Enhancers	HSMM	muscle
11	chr9:13720600-13722000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:13720800-13721200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:13720800-13721200	Weak transcription	NHLF	lung
14	chr9:13720800-13721400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:13720800-13729400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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