Variant report

Variant	rs9462464
Chromosome Location	chr6:38886122-38886123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38884806..38886853-chr6:38889455..38891873,2	K562	blood:
2	chr6:38885137..38887248-chr6:38897981..38900186,2	K562	blood:

Variant related genes	Relation type
ENSG00000231150	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11753074	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11753138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1332012	1.00[CEU][hapmap]
rs1332014	0.81[CEU][hapmap]
rs1537231	0.81[CEU][hapmap]
rs2235871	0.81[CEU][hapmap]
rs2273093	0.81[CEU][hapmap]
rs2281340	0.81[CEU][hapmap]
rs2281346	0.81[CEU][hapmap]
rs2395710	0.90[CEU][hapmap]
rs2894418	0.81[CEU][hapmap]
rs3734611	0.88[CHB][hapmap]
rs3857575	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4714202	0.90[CEU][hapmap]
rs4714203	0.90[CEU][hapmap]
rs4714208	0.81[CEU][hapmap]
rs506672	0.90[CEU][hapmap]
rs62398577	0.80[ASN][1000 genomes]
rs6458088	0.90[CEU][hapmap]
rs761384	0.81[CEU][hapmap]
rs7766930	0.81[CEU][hapmap]
rs9296273	0.81[CEU][hapmap]
rs9369100	0.81[CEU][hapmap]
rs9380817	0.81[CEU][hapmap]
rs9380818	0.90[CEU][hapmap]
rs9462460	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9462466	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462469	0.81[CEU][hapmap]
rs9470949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs9470950	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9470961	0.80[CEU][hapmap]
rs9470962	0.81[CEU][hapmap]

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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462918	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv602961	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9462464	ANKS1A	cis	parietal	SCAN
rs9462464	MED20	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38885200-38886600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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