Variant report

Variant	rs2365555
Chromosome Location	chr2:32280699-32280700
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	chr2:32279070..32283025-chr2:32287141..32290986,4	MCF-7	breast:
2	chr2:32277442..32284855-chr2:32286195..32291161,9	K562	blood:

Variant related genes	Relation type
ENSG00000021574	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10208246	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs10439444	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10490360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11124274	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11124275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124276	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124277	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11676938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs11678119	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap]
rs11681731	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683931	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11686061	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11691879	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465124	0.85[ASN][1000 genomes]
rs12465351	1.00[CHB][hapmap]
rs12474443	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12611678	0.83[ASN][1000 genomes]
rs12614686	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs12617289	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12617290	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12618002	0.82[ASN][1000 genomes]
rs12620922	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1272585	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12989936	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12992743	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997026	1.00[CHB][hapmap]
rs13000753	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007972	0.84[ASN][1000 genomes]
rs13008192	0.82[ASN][1000 genomes]
rs13017189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13022197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024004	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029752	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13033833	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13427170	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs13431540	0.83[ASN][1000 genomes]
rs160797	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs160801	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs17767988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1904489	0.81[ASN][1000 genomes]
rs212679	0.95[CEU][hapmap]
rs212687	0.86[CHD][hapmap]
rs212699	0.94[CEU][hapmap];0.87[TSI][hapmap]
rs212701	0.94[CEU][hapmap];0.87[TSI][hapmap]
rs212703	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs212714	0.87[TSI][hapmap]
rs212715	0.94[CEU][hapmap];0.91[CHB][hapmap]
rs212716	0.89[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs212717	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs212721	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs212724	0.94[CEU][hapmap]
rs212726	0.94[CEU][hapmap]
rs212727	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs212730	0.94[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap]
rs212731	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs212737	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs212738	1.00[CHB][hapmap]
rs212739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs212745	1.00[CEU][hapmap]
rs212746	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs212755	0.86[CHD][hapmap]
rs212758	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs212759	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs212760	1.00[CEU][hapmap]
rs212762	0.81[JPT][hapmap]
rs216538	0.94[ASN][1000 genomes]
rs216544	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2235134	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280969	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294176	0.81[ASN][1000 genomes]
rs2294179	0.83[ASN][1000 genomes]
rs2365558	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2366297	0.82[CHB][hapmap]
rs2366736	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs34856365	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35650265	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36014814	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752916	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3752917	0.81[ASN][1000 genomes]
rs3769602	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap]
rs3769604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769606	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs3851308	0.81[ASN][1000 genomes]
rs3851310	0.89[CEU][hapmap]
rs430759	0.94[CEU][hapmap];0.82[TSI][hapmap]
rs454119	0.89[ASN][1000 genomes]
rs455060	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs467523	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs469305	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs4952209	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs4952247	0.80[EUR][1000 genomes]
rs4952248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4952249	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952252	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs55730514	0.81[ASN][1000 genomes]
rs56208031	0.82[ASN][1000 genomes]
rs56740303	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62142080	0.82[ASN][1000 genomes]
rs6543647	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6543649	0.80[EUR][1000 genomes]
rs660393	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67157050	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716179	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs6717209	1.00[CHB][hapmap]
rs6723154	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs6725184	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.96[MEX][hapmap]
rs6737500	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738349	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6747488	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748621	0.89[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749336	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752375	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs6758024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6760105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6761417	0.82[ASN][1000 genomes]
rs678251	0.93[ASN][1000 genomes]
rs72862234	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7370704	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559964	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7561519	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7566162	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7572964	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs7573543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7575139	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577408	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7577696	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581032	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7581340	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7581432	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs7586448	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7588883	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs7600173	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600885	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7601267	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604559	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605242	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7608127	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608229	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677104	0.82[ASN][1000 genomes]
rs9750659	0.83[ASN][1000 genomes]
rs9752631	0.86[ASN][1000 genomes]
rs9752651	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2365555	SLC30A6	cis	cerebellum	SCAN
rs2365555	NLRC4	cis	lymphoblastoid	seeQTL
rs2365555	EHD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32275800-32287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:32278400-32283000	Weak transcription	HepG2	liver
3	chr2:32280200-32280800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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