Variant report

Variant	rs4426402
Chromosome Location	chr17:17977926-17977927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17972487..17976143-chr17:17976511..17979326,5	K562	blood:
2	chr17:17973806..17976094-chr17:17976515..17979331,5	K562	blood:
3	chr17:17967438..17969846-chr17:17976579..17978377,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141034	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1008135	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1101727	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11078406	0.94[ASW][hapmap];0.81[YRI][hapmap]
rs11078408	0.94[ASW][hapmap];0.85[CEU][hapmap];0.85[YRI][hapmap]
rs11078410	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11650021	0.85[EUR][1000 genomes]
rs11867241	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11870660	0.85[CEU][hapmap]
rs12150369	0.81[EUR][1000 genomes]
rs12939020	0.83[EUR][1000 genomes]
rs2056842	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955350	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2955353	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2955355	0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs2955356	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2955358	0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs2955359	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2955365	0.85[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs2955366	0.93[EUR][1000 genomes]
rs2955367	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955368	0.85[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2955372	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2955377	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[GIH][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs2955378	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs2955380	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2955381	0.94[CEU][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs2955383	0.95[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs2955384	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2955385	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2974998	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2974999	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4072738	0.89[CEU][hapmap]
rs4072739	0.89[CEU][hapmap]
rs4299203	0.85[CEU][hapmap]
rs4365346	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4365348	0.81[EUR][1000 genomes]
rs4368210	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[YRI][hapmap]
rs4410135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459604	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs4506967	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4506969	0.90[CEU][hapmap];0.89[YRI][hapmap]
rs4561528	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[YRI][hapmap]
rs4643387	0.87[EUR][1000 genomes]
rs4924832	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs4925125	0.94[ASW][hapmap];0.80[YRI][hapmap]
rs4925126	0.94[ASW][hapmap];0.81[YRI][hapmap]
rs4925135	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4925136	0.86[EUR][1000 genomes]
rs59518074	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62073573	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502632	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs6502633	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6502634	0.82[EUR][1000 genomes]
rs6502636	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502637	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6826	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs712267	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs712268	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7207461	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs7209003	0.95[CEU][hapmap]
rs7210400	0.86[EUR][1000 genomes]
rs7211714	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7212167	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs7212447	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7214002	0.85[YRI][hapmap]
rs7215524	0.81[EUR][1000 genomes]
rs721669	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7219320	0.81[GIH][hapmap]
rs7219324	0.89[CEU][hapmap]
rs7223696	0.80[EUR][1000 genomes]
rs7224047	0.83[EUR][1000 genomes]
rs7406744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7406982	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs741782	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7503738	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8066764	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8068175	0.85[CEU][hapmap]
rs8069811	0.82[EUR][1000 genomes]
rs8075189	0.95[CEU][hapmap]
rs8080602	0.95[CEU][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8082590	0.82[EUR][1000 genomes]
rs854763	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs854767	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854768	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854769	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854770	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854789	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs854790	1.00[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs854791	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs854792	0.81[EUR][1000 genomes]
rs854808	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854809	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854814	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854817	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs854818	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9303144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894138	0.86[EUR][1000 genomes]
rs9896837	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs9897761	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9899355	0.89[CEU][hapmap]
rs9913277	0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4426402	TOM1L2	cis	parietal	SCAN
rs4426402	SREBF1	cis	Whole Blood	GTEx
rs4426402	C17orf39	cis	cerebellum	SCAN
rs4426402	TOM1L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:17971400-17978200	Weak transcription	Brain Anterior Caudate	brain
3	chr17:17974600-17979200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:17974600-17984400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:17974600-17986400	Weak transcription	Placenta	Placenta
6	chr17:17974800-17978000	Weak transcription	A549	lung
7	chr17:17977800-17978000	Enhancers	K562	blood
8	chr17:17977800-17978400	Enhancers	HepG2	liver

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