Variant report

Variant	rs11934405
Chromosome Location	chr4:175270804-175270805
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	chr4:175270741..175272762-chr4:175708411..175710972,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1001914	1.00[LWK][hapmap]
rs10446854	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11939414	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11944262	0.82[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs11946084	0.86[ASN][1000 genomes]
rs13111067	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13112711	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13125731	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13151156	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2332836	0.80[GIH][hapmap]
rs34066344	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34274380	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34369193	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34698083	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34765808	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34988464	0.86[ASN][1000 genomes]
rs35377027	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35473266	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35567270	0.86[EUR][1000 genomes]
rs35918158	0.93[ASN][1000 genomes]
rs4280712	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4293767	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4306937	0.86[EUR][1000 genomes]
rs4408938	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4408939	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4428259	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4447835	0.86[EUR][1000 genomes]
rs4452408	0.86[EUR][1000 genomes]
rs4458430	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4469047	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4695777	0.86[EUR][1000 genomes]
rs4695923	0.86[ASN][1000 genomes]
rs4695926	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695927	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695928	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695931	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56041548	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58895800	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67509565	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6812756	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6812772	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6814901	0.86[EUR][1000 genomes]
rs6817902	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6824643	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs6831848	0.86[EUR][1000 genomes]
rs6851312	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs6855058	0.86[EUR][1000 genomes]
rs6855451	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72702274	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72702283	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7656670	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11934405	KIAA1712	cis	cerebellum	SCAN
rs11934405	KIAA1712	cis	parietal	SCAN
rs11934405	FBXO8	cis	cerebellum	SCAN
rs11934405	FBXO8	cis	parietal	SCAN
rs11934405	CEP44	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175267600-175273400	Weak transcription	Right Ventricle	heart
2	chr4:175270400-175271200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:175270600-175271000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:175270600-175271200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:175270600-175271600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr4:175270800-175271200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr4:175270800-175272000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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