Variant report

Variant	rs4845679
Chromosome Location	chr1:154861187-154861188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154854688..154856959-chr1:154860372..154862285,3	K562	blood:
2	chr1:154854131..154858067-chr1:154858764..154862484,5	K562	blood:
3	chr1:154598479..154600465-chr1:154859924..154861942,2	MCF-7	breast:
4	chr1:154856910..154859429-chr1:154860330..154863097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160710	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1007170	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10796934	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10796935	0.95[ASN][1000 genomes]
rs10908444	0.88[ASN][1000 genomes]
rs10908445	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908446	1.00[ASN][1000 genomes]
rs10908447	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1109815	0.91[ASN][1000 genomes]
rs11264278	0.83[ASN][1000 genomes]
rs11264280	0.89[ASN][1000 genomes]
rs11264281	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264282	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264283	1.00[ASN][1000 genomes]
rs11264284	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264290	0.91[ASN][1000 genomes]
rs11264291	0.81[AMR][1000 genomes]
rs12036859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069356	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12095061	0.91[CEU][hapmap];0.91[ASN][1000 genomes]
rs12130132	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144978	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1580943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976559	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1977879	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061690	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2102423	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2135219	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2174507	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2335407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2335408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs2335409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4240874	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240875	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4339857	0.95[ASN][1000 genomes]
rs4578216	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4845398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845399	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845400	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845678	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845680	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845681	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845682	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845683	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845685	0.90[ASN][1000 genomes]
rs4845687	0.92[ASN][1000 genomes]
rs4845688	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845689	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845690	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[ASN][1000 genomes]
rs4845691	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845693	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845694	0.91[ASN][1000 genomes]
rs4845695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4845696	0.91[ASN][1000 genomes]
rs6656435	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6656494	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669791	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674853	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683557	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686873	0.91[ASN][1000 genomes]
rs6699043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs6699080	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs705094	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs72702224	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7528532	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544528	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs869506	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877343	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs883718	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs906593	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9793588	0.88[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4845679	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL
rs4845679	C1orf92	cis	cerebellum	SCAN
rs4845679	ENSA	cis	parietal	SCAN
rs4845679	KCNN3	cis	cerebellum	SCAN
rs4845679	UBAP2L	cis	parietal	SCAN
rs4845679	OAZ3	cis	parietal	SCAN
rs4845679	KCNN3	cis	parietal	SCAN
rs4845679	OTUD7B	cis	cerebellum	SCAN
rs4845679	PBXIP1	cis	lymphoblastoid	seeQTL
rs4845679	RIT1	cis	cerebellum	SCAN
rs4845679	INTS3	cis	parietal	SCAN
rs4845679	S100A3	cis	cerebellum	SCAN
rs4845679	PBXIP1	cis	normal skin	skin_eQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154856400-154861800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:154858000-154863800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154859400-154863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:154859400-154863600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:154859600-154861200	Weak transcription	Right Atrium	heart
6	chr1:154859600-154863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:154859600-154863800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:154860200-154862200	Enhancers	K562	blood
9	chr1:154860400-154861200	Enhancers	Fetal Heart	heart
10	chr1:154860600-154862200	Enhancers	Spleen	Spleen

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