Variant report

Variant	rs6461140
Chromosome Location	chr7:14871856-14871857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10085416	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10085569	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10225316	0.91[EUR][1000 genomes]
rs10241696	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10276530	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10487781	0.94[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1988291	0.90[EUR][1000 genomes]
rs2041409	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2109499	0.95[ASN][1000 genomes]
rs2109500	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2191481	0.94[ASN][1000 genomes]
rs2191482	0.83[ASN][1000 genomes]
rs2358070	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34561304	0.92[EUR][1000 genomes]
rs4721382	0.91[EUR][1000 genomes]
rs58021112	0.88[EUR][1000 genomes]
rs60142008	0.91[EUR][1000 genomes]
rs60557254	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6461137	0.94[ASN][1000 genomes]
rs7784739	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7790062	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7793794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7806933	0.94[ASN][1000 genomes]
rs929522	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929523	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs994369	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1020722	chr7:14792114-14871907	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6461140	HDAC9	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14855800-14873200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:14870400-14873200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:14871000-14873000	Weak transcription	Osteobl	bone
4	chr7:14871200-14873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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