Variant report

Variant	rs17161618
Chromosome Location	chr7:98801704-98801705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98740092..98741933-chr7:98801058..98802598,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198742	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10499949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705032	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12705033	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12705034	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs12705035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705036	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[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705038	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705039	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705041	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap]
rs12705042	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap]
rs12705045	1.00[CEU][hapmap]
rs12705047	1.00[CEU][hapmap]
rs12705049	1.00[CEU][hapmap]
rs13221427	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13224433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13236786	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236896	0.90[EUR][1000 genomes]
rs13237093	0.92[EUR][1000 genomes]
rs13238146	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13239506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242894	1.00[CEU][hapmap]
rs13244043	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13244327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13244579	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13244583	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13244592	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13247718	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13247877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13310182	1.00[CEU][hapmap]
rs13310534	1.00[CEU][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs16867592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17161611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17161615	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17161617	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[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17161622	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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34088480	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34221671	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34250243	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34350957	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34715870	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34724557	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34929886	0.90[ASN][1000 genomes]
rs35312766	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35511099	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35597916	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35611495	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35615419	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61749907	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66785725	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66931650	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67422346	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67723713	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67749476	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68076840	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71567531	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73401379	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73401390	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73403103	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73403107	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7778995	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7779268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7779342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7783606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7783618	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7787830	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[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7788790	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[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7789312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7793425	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[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7793510	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7795644	0.83[MEX][hapmap]
rs7798877	0.82[CHD][hapmap]
rs7805070	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7806230	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7808942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7809188	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[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17161618	USP3	trans	brain	seeQTL
rs17161618	ESPNL	trans	brain	seeQTL
rs17161618	PCP2	trans	brain	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98792200-98803600	Weak transcription	Stomach Mucosa	stomach
2	chr7:98801000-98801800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:98801400-98807600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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