Variant report

Variant	rs12551877
Chromosome Location	chr9:27142888-27142889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10511799	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10511804	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12552280	0.90[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs12552985	0.90[CEU][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12555409	0.85[AFR][1000 genomes]
rs13285984	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes]
rs13293515	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13296438	0.86[AMR][1000 genomes]
rs17694837	0.84[CEU][hapmap];0.85[AFR][1000 genomes]
rs17695057	1.00[CEU][hapmap];0.91[AMR][1000 genomes]
rs35174672	0.84[AMR][1000 genomes]
rs4879912	0.81[AFR][1000 genomes]
rs67069851	0.83[AFR][1000 genomes]
rs716676	1.00[CEU][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs7852018	0.84[AMR][1000 genomes]
rs7853262	1.00[CEU][hapmap];0.90[MEX][hapmap];0.91[AMR][1000 genomes]
rs7855848	0.90[CEU][hapmap]
rs7862217	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv613945	chr9:27121906-27148475	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv892863	chr9:27138898-27170934	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12551877	TEK	cis	parietal	SCAN
rs12551877	MOBKL2B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27122800-27150800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:27129800-27144600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:27131400-27143000	Weak transcription	Left Ventricle	heart
4	chr9:27134000-27145200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:27138400-27144400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:27142200-27144400	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:27142400-27143200	Enhancers	Right Atrium	heart
8	chr9:27142400-27143400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:27142600-27143200	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:27142800-27144000	Enhancers	HUVEC	blood vessel

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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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