Variant report

Variant	rs11866859
Chromosome Location	chr16:71478888-71478889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71478885..71480600-chr16:71492072..71493651,2	K562	blood:
2	chr16:71474535..71476293-chr16:71477936..71479872,2	MCF-7	breast:
3	chr16:71477364..71480165-chr16:71494025..71496473,2	K562	blood:
4	chr16:71477849..71480634-chr16:71486623..71488977,2	K562	blood:

Variant related genes	Relation type
ENSG00000247324	Chromatin interaction
ENSG00000167377	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10468265	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12934739	0.84[EUR][1000 genomes]
rs12935725	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs13333985	0.96[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs13336809	1.00[ASN][1000 genomes]
rs16972266	1.00[ASN][1000 genomes]
rs16972663	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16972805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972808	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16973000	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16973112	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16973190	1.00[ASN][1000 genomes]
rs2052873	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs310335	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs3886947	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4258624	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs4644867	0.94[EUR][1000 genomes]
rs56222754	1.00[ASN][1000 genomes]
rs61171207	1.00[ASN][1000 genomes]
rs7188021	1.00[ASN][1000 genomes]
rs7188475	0.96[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7188858	0.93[EUR][1000 genomes]
rs7197127	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72791971	1.00[ASN][1000 genomes]
rs72795864	1.00[ASN][1000 genomes]
rs72795869	1.00[ASN][1000 genomes]
rs72795881	1.00[ASN][1000 genomes]
rs7499392	0.93[EUR][1000 genomes]
rs8044168	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8049040	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8050135	1.00[ASN][1000 genomes]
rs8051439	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8054221	0.82[EUR][1000 genomes]
rs8056735	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8060176	0.83[EUR][1000 genomes]
rs9940485	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989377	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv1064435	chr16:71440719-71488771	Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11866859	CMTM1	cis	cerebellum	SCAN
rs11866859	ZNF23	cis	parietal	SCAN
rs11866859	SNTB2	cis	cerebellum	SCAN
rs11866859	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx
rs11866859	CBFB	cis	parietal	SCAN
rs11866859	HSF4	cis	parietal	SCAN
rs11866859	TPPP3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71475000-71479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:71476800-71482000	Weak transcription	HepG2	liver
3	chr16:71478200-71482200	Weak transcription	Fetal Heart	heart
4	chr16:71478200-71487800	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr16:71478400-71480600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr16:71478400-71481000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:71478600-71482000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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