Variant report

Variant	rs7800418
Chromosome Location	chr7:26606005-26606006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10231724	0.86[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs10244803	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10252484	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1029556	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs1029557	0.83[JPT][hapmap]
rs1029558	0.81[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs13223498	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13241848	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2190188	0.87[EUR][1000 genomes]
rs4461797	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs730558	0.81[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs757805	0.88[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs757806	0.87[EUR][1000 genomes]
rs757807	0.87[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs757808	0.84[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs757809	0.95[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs757810	0.82[EUR][1000 genomes]
rs757811	0.82[EUR][1000 genomes]
rs757812	0.87[EUR][1000 genomes]
rs7788433	0.87[EUR][1000 genomes]
rs882541	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.86[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	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cognitive function	24684796	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7800418	HOXA11	cis	parietal	SCAN
rs7800418	IL6	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26593600-26607000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:26601600-26606600	Weak transcription	Hela-S3	cervix

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