Variant report

Variant	rs10490241
Chromosome Location	chr2:50332310-50332311
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57913850..57916261-chr2:50331209..50333765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1037428	0.87[EUR][1000 genomes]
rs10490243	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs10490244	0.87[EUR][1000 genomes]
rs11887484	0.81[AFR][1000 genomes]
rs11898302	0.81[AFR][1000 genomes]
rs12151722	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12469244	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12470002	1.00[CEU][hapmap]
rs12472712	1.00[CEU][hapmap]
rs12472743	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs12473119	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12474335	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12476530	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12476825	1.00[CEU][hapmap]
rs12477934	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12478603	0.89[CEU][hapmap]
rs12478732	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12479057	0.81[EUR][1000 genomes]
rs12613363	1.00[CEU][hapmap]
rs12613778	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622858	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12986904	1.00[CEU][hapmap]
rs1377233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1377237	1.00[CEU][hapmap]
rs1452762	0.81[YRI][hapmap]
rs1452764	0.81[YRI][hapmap]
rs1452766	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1452767	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1452768	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1452778	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1452779	1.00[CEU][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes]
rs1452780	0.95[EUR][1000 genomes]
rs1452781	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1452783	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1523355	0.81[YRI][hapmap]
rs1563024	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs1563026	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs1563027	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17039764	1.00[CEU][hapmap]
rs17039801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17039807	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17039848	0.84[EUR][1000 genomes]
rs17040210	0.84[CEU][hapmap]
rs1840074	0.81[EUR][1000 genomes]
rs1961358	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2011317	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2045003	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs2123388	1.00[CEU][hapmap]
rs2218979	1.00[CEU][hapmap]
rs4032305	0.84[EUR][1000 genomes]
rs4641977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs4971554	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4971646	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4971648	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4971649	0.81[CHB][hapmap]
rs6545149	1.00[CEU][hapmap]
rs6545155	0.89[CEU][hapmap]
rs6716404	0.89[GIH][hapmap]
rs72874683	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72878113	0.98[ASN][1000 genomes]
rs72878115	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72878120	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72878122	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72878124	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs896683	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs896684	0.95[CEU][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs896685	0.81[AFR][1000 genomes]
rs921572	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921573	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs930752	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9309176	0.86[YRI][hapmap]
rs962332	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs962333	0.88[EUR][1000 genomes]
rs970896	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9917277	0.86[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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2755683	chr2:50307245-50345280	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2756107	chr2:50307245-50440043	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv948833	chr2:50307245-50459077	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2756536	chr2:50313811-50375695	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1002344	chr2:50326207-50518933	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv535692	chr2:50326207-50518933	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10490241	NRXN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50330400-50345600	Weak transcription	Fetal Brain Male	brain

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