Variant report

Variant	rs12699651
Chromosome Location	chr7:14678999-14679000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10950533	0.80[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs1404618	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1404621	0.80[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4409300	0.92[CEU][hapmap]
rs6953043	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6953418	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6954056	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6968775	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7807865	0.90[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs7811333	0.96[CEU][hapmap];0.82[CHD][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949033	chr7:14086106-14860323	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1031041	chr7:14624127-14999201	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538741	chr7:14624127-14999201	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1015777	chr7:14661754-14730811	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12699651	HDAC9	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14675000-14679600	Enhancers	Liver	Liver
2	chr7:14678200-14679600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr7:14678200-14680400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:14678600-14679000	Weak transcription	Stomach Mucosa	stomach
5	chr7:14678600-14679200	Weak transcription	Left Ventricle	heart
6	chr7:14678800-14679000	Enhancers	Duodenum Mucosa	Duodenum
7	chr7:14678800-14680000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr7:14678800-14680400	Enhancers	HMEC	breast

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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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