Variant report

Variant	rs10236011
Chromosome Location	chr7:14642523-14642524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10156103	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs10227646	0.95[ASN][1000 genomes]
rs10246717	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10246968	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs10251321	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10254418	0.81[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs10256605	0.84[CHD][hapmap];0.85[AMR][1000 genomes]
rs10273764	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs11768578	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773345	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1189365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11983714	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs12670550	0.84[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1357864	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1357865	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1357866	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357867	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1357868	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1357869	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1431522	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap]
rs1474385	0.97[ASN][1000 genomes]
rs1525083	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525088	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs1525089	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1560478	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs17150062	0.84[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs17168296	0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17168298	0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[ASN][1000 genomes]
rs17168299	0.84[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs17595206	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs17595234	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs17602988	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs17603201	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17603341	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2049450	0.87[CEU][hapmap]
rs3795245	0.96[ASN][1000 genomes]
rs3920402	0.83[AMR][1000 genomes]
rs3951243	0.95[ASN][1000 genomes]
rs4537212	0.95[ASN][1000 genomes]
rs55681155	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62443555	0.94[ASN][1000 genomes]
rs62443556	0.94[ASN][1000 genomes]
rs62443557	0.94[ASN][1000 genomes]
rs66473448	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6944740	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6947430	0.83[AMR][1000 genomes]
rs6951414	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6956742	0.80[CEU][hapmap]
rs6960433	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6969050	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs73059484	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73059497	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7777504	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs7796807	0.90[ASN][1000 genomes]
rs7809502	0.97[ASN][1000 genomes]
rs7810871	0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs879693	0.88[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs940690	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs940691	0.98[ASN][1000 genomes]
rs953604	0.90[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs953605	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][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	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	nsv887710	chr7:14587948-14653702	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv887711	chr7:14619026-14671325	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10236011	HDAC9	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14636600-14644200	Weak transcription	HMEC	breast
2	chr7:14636800-14644400	Weak transcription	Osteobl	bone
3	chr7:14638000-14645800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:14640000-14644000	Weak transcription	Fetal Heart	heart
5	chr7:14641600-14648800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:14642200-14644800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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