Variant report

Variant	rs4364874
Chromosome Location	chr1:154167788-154167789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
2	chr1:154161421..154168420-chr1:154191340..154198003,13	MCF-7	breast:
3	chr1:153934849..153937744-chr1:154167271..154169593,2	MCF-7	breast:
4	chr1:154154241..154157353-chr1:154161640..154168172,9	MCF-7	breast:
5	chr1:154166360..154171923-chr1:154189576..154194577,9	K562	blood:
6	chr1:154162762..154164627-chr1:154167547..154169512,2	K562	blood:
7	chr1:154162854..154164787-chr1:154165144..154168912,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143612	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143570	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10797058	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10797061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10908739	0.82[CEU][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10908751	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265285	0.90[EUR][1000 genomes]
rs1194580	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194582	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194599	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194603	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044616	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12063830	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12095767	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12354278	1.00[JPT][hapmap]
rs13796	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1591902	1.00[CHB][hapmap]
rs1832582	1.00[JPT][hapmap]
rs2220390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2790686	0.82[CHB][hapmap]
rs2841108	0.82[CHB][hapmap]
rs3001365	0.82[CHB][hapmap]
rs4072431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[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]
rs4393149	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4400599	0.81[GIH][hapmap]
rs4540651	0.84[YRI][hapmap]
rs4579747	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845364	0.86[ASW][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs4845605	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap]
rs4845609	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845610	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6667222	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6680947	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7516809	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7526644	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7533952	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9803862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9804045	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9943097	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4364874	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs4364874	C1orf43	cis	parietal	SCAN
rs4364874	CKS1B	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154159000-154184400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:154160400-154169400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:154163200-154169400	Weak transcription	Fetal Heart	heart
4	chr1:154163800-154178800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:154164600-154178800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:154164800-154178200	Weak transcription	Lung	lung
7	chr1:154164800-154178400	Weak transcription	Ovary	ovary
8	chr1:154165200-154177800	Weak transcription	Placenta	Placenta
9	chr1:154165800-154178400	Weak transcription	Psoas Muscle	Psoas
10	chr1:154166400-154167800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:154166800-154169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:154166800-154169000	Weak transcription	HMEC	breast
13	chr1:154166800-154169200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:154166800-154169400	Weak transcription	Hela-S3	cervix
15	chr1:154166800-154169600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:154166800-154171800	Weak transcription	HSMM	muscle
17	chr1:154166800-154171800	Weak transcription	HSMMtube	muscle
18	chr1:154166800-154172000	Weak transcription	Pancreas	Pancrea
19	chr1:154166800-154177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:154167000-154169000	Weak transcription	NHEK	skin
21	chr1:154167000-154169600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:154167000-154169800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:154167000-154178600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:154167200-154177800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:154167400-154171600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:154167400-154171800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:154167600-154167800	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:154167600-154168000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:154167600-154168200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:154167600-154168200	Enhancers	HepG2	liver
31	chr1:154167600-154171600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:154167600-154171800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:154167600-154177200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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