Variant report

Variant	rs6592177
Chromosome Location	chr11:84067997-84067998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10501559	0.91[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs10792755	0.82[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10898226	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898227	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11822426	0.85[YRI][hapmap]
rs1559854	0.92[ASW][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs3914464	0.85[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4310638	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs4547118	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489716	0.89[JPT][hapmap]
rs4943892	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4943893	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4944487	0.88[EUR][1000 genomes]
rs504196	0.83[LWK][hapmap]
rs567263	0.83[JPT][hapmap]
rs568789	0.89[JPT][hapmap]
rs61897669	0.91[ASN][1000 genomes]
rs6592176	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs6592179	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs672796	0.94[JPT][hapmap]
rs7108323	0.82[AMR][1000 genomes]
rs7115400	0.95[CEU][hapmap]
rs7117729	0.95[CEU][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7118287	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7121832	0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7124614	0.84[AMR][1000 genomes]
rs7127845	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs7128063	0.92[ASW][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs7128524	0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7942296	0.85[ASW][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs7947614	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948410	chr11:83918339-84812001	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1038641	chr11:83996453-84334045	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv541103	chr11:83996453-84334045	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1049696	chr11:84039547-84116297	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv898031	chr11:84060342-84379671	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1047030	chr11:84067493-84187274	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1041755	chr11:84067493-84315623	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv541104	chr11:84067493-84315623	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6592177	TMEM126B	cis	parietal	SCAN
rs6592177	CCDC90B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:84067600-84071600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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