Variant report

Variant	rs455060
Chromosome Location	chr2:32475109-32475110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32469608..32472298-chr2:32474844..32477443,2	K562	blood:
2	chr2:32473322..32475568-chr2:32480051..32482109,2	K562	blood:
3	chr2:32474270..32479271-chr2:32479320..32483848,6	K562	blood:
4	chr2:32473864..32476100-chr2:32581947..32583463,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115760	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10490360	0.94[CEU][hapmap]
rs11124275	0.94[CEU][hapmap]
rs11124276	0.83[EUR][1000 genomes]
rs11124277	0.83[EUR][1000 genomes]
rs11676938	0.89[CEU][hapmap]
rs11681731	0.85[EUR][1000 genomes]
rs11686061	0.83[EUR][1000 genomes]
rs12474443	0.82[EUR][1000 genomes]
rs12614686	0.81[LWK][hapmap]
rs12617289	0.85[EUR][1000 genomes]
rs12617290	0.84[EUR][1000 genomes]
rs1265341	0.86[EUR][1000 genomes]
rs13017189	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs13022197	0.94[CEU][hapmap];0.80[LWK][hapmap];0.85[EUR][1000 genomes]
rs177083	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs17767988	0.94[CEU][hapmap]
rs212678	0.85[EUR][1000 genomes]
rs212679	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs212695	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212698	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs212699	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs212700	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212701	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs212704	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[ASN][1000 genomes]
rs212706	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[ASN][1000 genomes]
rs212707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs212708	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs212713	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212714	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212715	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs212716	0.94[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs212717	1.00[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs212718	0.93[EUR][1000 genomes]
rs212721	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212722	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212723	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212725	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212728	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212732	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs212733	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212734	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212735	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212737	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212739	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs212745	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs212746	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs212758	0.94[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs212759	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs212760	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2235134	0.85[EUR][1000 genomes]
rs2280967	0.94[CEU][hapmap];0.93[TSI][hapmap]
rs2365555	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs2365558	0.84[EUR][1000 genomes]
rs2566483	0.91[EUR][1000 genomes]
rs374743	0.89[EUR][1000 genomes]
rs3769604	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3769606	0.89[CEU][hapmap];0.83[LWK][hapmap]
rs385076	0.83[CEU][hapmap]
rs3851310	0.82[CEU][hapmap]
rs408813	0.91[EUR][1000 genomes]
rs428002	0.90[EUR][1000 genomes]
rs430759	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs435572	0.89[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs443609	0.94[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs466126	0.89[EUR][1000 genomes]
rs469305	0.80[CEU][hapmap]
rs479333	0.94[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.82[EUR][1000 genomes]
rs494569	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952247	0.83[EUR][1000 genomes]
rs4952248	0.94[CEU][hapmap]
rs4952249	0.81[EUR][1000 genomes]
rs4952250	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs57903075	0.98[ASN][1000 genomes]
rs59966205	0.91[EUR][1000 genomes]
rs6543649	0.84[EUR][1000 genomes]
rs659239	0.94[CEU][hapmap];0.81[LWK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs6725184	0.94[CEU][hapmap];0.81[LWK][hapmap]
rs6738349	0.80[EUR][1000 genomes]
rs6747488	0.82[EUR][1000 genomes]
rs6758024	0.94[CEU][hapmap]
rs6760105	0.94[CEU][hapmap];0.93[TSI][hapmap]
rs7559964	0.83[EUR][1000 genomes]
rs7561519	0.89[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs7566162	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7573543	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs7577696	0.94[CEU][hapmap];0.93[TSI][hapmap]
rs7581032	0.83[EUR][1000 genomes]
rs7581340	0.85[CEU][hapmap];0.81[LWK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs7605242	0.89[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv2667	chr2:32444810-32489755	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1002120	chr2:32470452-32539443	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1004279	chr2:32470452-32543369	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs455060	EHD3	cis	parietal	SCAN
rs455060	SLC30A6	cis	cerebellum	SCAN
rs455060	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32443000-32483600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:32443200-32483800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:32447400-32483800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:32448800-32475600	Weak transcription	Lung	lung
5	chr2:32448800-32484800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:32451600-32475600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:32452000-32475400	Weak transcription	Spleen	Spleen
8	chr2:32452200-32479400	Weak transcription	Adipose Nuclei	Adipose
9	chr2:32460000-32477000	Weak transcription	Placenta	Placenta
10	chr2:32463600-32487000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:32465000-32475400	Weak transcription	Primary B cells from cord blood	blood
12	chr2:32470600-32477000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:32474200-32476600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:32474400-32476800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:32474600-32475200	Enhancers	HepG2	liver
16	chr2:32475000-32475400	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:32475000-32481200	Weak transcription	Fetal Heart	heart

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