Variant report

Variant	rs6564434
Chromosome Location	chr16:77396835-77396836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10514411	0.86[CEU][hapmap]
rs10514412	0.86[CEU][hapmap]
rs10514415	0.80[CHB][hapmap]
rs11149981	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12051144	0.85[EUR][1000 genomes]
rs12051395	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12051418	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs12448640	0.84[CHB][hapmap]
rs12597784	0.84[EUR][1000 genomes]
rs12597837	0.84[EUR][1000 genomes]
rs12598504	0.85[CHB][hapmap]
rs12598787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12599131	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs12599448	0.85[CHB][hapmap]
rs12600056	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12932499	0.85[CHB][hapmap]
rs1318020	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1318021	0.80[CHB][hapmap]
rs1392607	0.80[CHB][hapmap]
rs1392608	0.80[CHB][hapmap]
rs17687224	0.86[CEU][hapmap]
rs17713725	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17769937	0.93[CEU][hapmap]
rs1909802	0.89[CHB][hapmap]
rs2062578	0.93[CEU][hapmap]
rs2246607	0.85[CHB][hapmap]
rs2434888	0.89[CHB][hapmap]
rs2434889	0.83[CHB][hapmap]
rs2562112	0.80[CHB][hapmap]
rs2562115	0.84[CHB][hapmap]
rs2650905	0.85[CHB][hapmap]
rs2650907	0.80[CHB][hapmap]
rs2650908	0.85[CHB][hapmap]
rs7192938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72487959	0.85[EUR][1000 genomes]
rs8057114	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs866924	0.84[CHB][hapmap]
rs866925	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs891134	0.80[CHB][hapmap]
rs937585	0.80[CHB][hapmap]
rs9746317	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2761916	chr16:77277005-77555833	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1059194	chr16:77281068-77745928	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv542969	chr16:77281068-77745928	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv2751613	chr16:77373039-77444872	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6564434	ADAMTS18	cis	parietal	SCAN
rs6564434	FA2H	cis	cerebellum	SCAN
rs6564434	ADAMTS18	cis	cerebellum	SCAN
rs6564434	KCNQ4	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77378400-77399600	Weak transcription	Adipose Nuclei	Adipose
2	chr16:77393400-77398200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:77393800-77397600	Weak transcription	HUVEC	blood vessel
4	chr16:77394200-77401600	Weak transcription	Ovary	ovary
5	chr16:77395800-77398000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:77396000-77398200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:77396600-77397000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr16:77396800-77401400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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