Variant report

Variant	rs4266420
Chromosome Location	chr5:178137161-178137162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178135058..178137507-chr5:178144599..178147677,3	MCF-7	breast:
2	chr5:178135141..178137270-chr5:178138560..178140664,2	K562	blood:
3	chr5:178130386..178132471-chr5:178136423..178139272,2	K562	blood:
4	chr5:178135337..178138008-chr5:178419462..178422313,2	K562	blood:

Variant related genes	Relation type
ENSG00000113262	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10043035	0.86[EUR][1000 genomes]
rs1071881	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1071882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1071883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132336	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1132338	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11739893	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742156	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11742176	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11742808	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11743893	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11747097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11747232	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11747390	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[LWK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11748495	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748497	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11749438	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11750409	0.87[EUR][1000 genomes]
rs13173130	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13186580	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17184281	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17184302	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17184344	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17652247	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169762	0.80[ASN][1000 genomes]
rs2335443	0.81[ASN][1000 genomes]
rs34601045	0.87[EUR][1000 genomes]
rs34651317	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34703961	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34981407	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35007468	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35850587	0.87[EUR][1000 genomes]
rs4470778	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55774261	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55818572	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55974982	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56027952	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56070635	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56159071	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56206101	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56236920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58549512	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59259518	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61247551	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62392825	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392826	0.87[ASN][1000 genomes]
rs62392827	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62392831	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62392832	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62392833	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62392839	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62392842	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62392854	0.83[EUR][1000 genomes]
rs66947564	0.84[EUR][1000 genomes]
rs6866344	0.80[ASN][1000 genomes]
rs6870021	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6873150	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6890741	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6896799	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71611460	0.81[EUR][1000 genomes]
rs72812613	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7732764	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4266420	ZNF354A	cis	parietal	SCAN
rs4266420	FAM193B	cis	parietal	SCAN
rs4266420	ZNF354A	cis	cerebellum	SCAN
rs4266420	ZNF354A	cis	Thyroid	GTEx
rs4266420	ZNF354A	cis	lymphoblastoid	seeQTL
rs4266420	HK3	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178130000-178150600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr5:178135400-178150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:178135800-178138000	ZNF genes & repeats	Brain Hippocampus Middle	brain
4	chr5:178135800-178147600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
5	chr5:178135800-178155600	ZNF genes & repeats	Liver	Liver
6	chr5:178136200-178155200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr5:178136400-178138600	Weak transcription	Fetal Heart	heart
8	chr5:178136600-178141000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
9	chr5:178136800-178150400	ZNF genes & repeats	Brain Substantia Nigra	brain
10	chr5:178136800-178150600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:178136800-178152800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr5:178137000-178149800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
13	chr5:178137000-178150600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:178137000-178150600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

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