Variant report

Variant	rs13319969
Chromosome Location	chr3:160827839-160827840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160825465..160827951-chr3:160887384..160889097,2	MCF-7	breast:
2	chr3:160826732..160829358-chr3:160938079..160940393,2	K562	blood:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1045448	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12107243	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12488037	0.85[AMR][1000 genomes]
rs12488621	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12494133	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs12494844	0.91[CHD][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs13318781	0.91[CHD][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs13320863	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13325518	0.89[CEU][hapmap]
rs1599380	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599384	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1599391	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831868	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1947685	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1947686	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2231252	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279106	1.00[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs28623696	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35152606	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35440670	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35446590	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35599916	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36105583	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4339146	0.86[EUR][1000 genomes]
rs4443220	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4465984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4487256	0.83[JPT][hapmap]
rs4490410	0.92[JPT][hapmap];0.82[AMR][1000 genomes]
rs62278031	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441352	0.88[EUR][1000 genomes]
rs6441353	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6763838	0.95[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs6795977	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68159406	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs721657	0.88[EUR][1000 genomes]
rs731363	0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73160351	0.82[AMR][1000 genomes]
rs7429731	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7630896	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7634115	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649954	0.95[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs898683	0.95[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs898684	0.95[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs898685	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs9290067	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9290068	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9810737	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812083	0.84[JPT][hapmap]
rs9813136	0.92[EUR][1000 genomes]
rs9817747	0.92[ASN][1000 genomes]
rs9818516	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9824308	0.95[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9824501	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9825118	0.92[JPT][hapmap]
rs9827833	0.84[JPT][hapmap]
rs9828189	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs9828205	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9829882	0.95[EUR][1000 genomes]
rs9830139	0.95[EUR][1000 genomes]
rs9834751	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836074	0.84[EUR][1000 genomes]
rs9839404	0.84[JPT][hapmap]
rs9840389	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9842281	0.82[AMR][1000 genomes]
rs9846316	0.91[JPT][hapmap]
rs9851292	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9858399	0.82[AMR][1000 genomes]
rs9861850	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs9862258	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864145	0.88[EUR][1000 genomes]
rs9876553	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs9878365	0.84[AMR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats 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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13319969	IFT20	trans	brain	seeQTL
rs13319969	KAT2A	trans	brain	seeQTL
rs13319969	HELZ	trans	brain	seeQTL
rs13319969	B3GALNT1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160823200-160832800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:160823400-160828800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:160823400-160829600	Weak transcription	Aorta	Aorta
4	chr3:160823600-160828200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:160823600-160829200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:160823800-160828200	Weak transcription	Right Ventricle	heart
7	chr3:160823800-160830400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:160824200-160830800	Weak transcription	Ovary	ovary
9	chr3:160826200-160829000	Weak transcription	Fetal Heart	heart
10	chr3:160826800-160834400	Weak transcription	Left Ventricle	heart

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