Variant report

Variant	rs11973605
Chromosome Location	chr7:25607805-25607806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10486406	0.84[ASN][1000 genomes]
rs10951078	0.84[ASN][1000 genomes]
rs11973587	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11973620	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12669889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12670768	0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs1354264	0.84[ASN][1000 genomes]
rs1553399	0.84[ASN][1000 genomes]
rs16873895	0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs16873899	0.84[ASN][1000 genomes]
rs16873909	0.80[ASN][1000 genomes]
rs17151904	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1818146	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs28473276	0.81[ASN][1000 genomes]
rs2952523	0.88[ASN][1000 genomes]
rs2960821	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs62454590	0.82[ASN][1000 genomes]
rs62454591	0.84[ASN][1000 genomes]
rs62454592	0.84[ASN][1000 genomes]
rs739622	0.84[ASN][1000 genomes]
rs975369	0.82[ASN][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	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
4	nsv525378	chr7:25605725-25615221	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv526019	chr7:25606120-25615221	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv527227	chr7:25606120-25615221	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv1797873	chr7:25606956-25615898	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11973605	HOXA9	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25604600-25608200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:25604800-25608200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:25606200-25608000	Weak transcription	Fetal Lung	lung
4	chr7:25607400-25608000	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr7:25607800-25608800	Enhancers	Stomach Mucosa	stomach

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