Variant report

Variant	rs2405065
Chromosome Location	chr1:224535420-224535421
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	chr1:224533712..224537182-chr1:224543123..224546153,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10158063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10733024	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10737442	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737443	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799562	0.82[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799563	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799566	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799567	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799568	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916577	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916599	0.80[ASN][1000 genomes]
rs11802486	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11811730	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806742	1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001712	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001713	0.96[EUR][1000 genomes]
rs2404783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404856	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404857	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404858	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404859	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405062	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405067	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405070	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2896990	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896992	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2897054	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3754090	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767724	0.98[ASN][1000 genomes]
rs3767725	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146966	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4256779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420060	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4457542	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4628473	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653575	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653581	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654011	0.86[ASN][1000 genomes]
rs4654017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4654019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654022	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs4654023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654032	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654033	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654034	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675086	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55980628	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57324770	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58855990	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59106681	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426088	0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6426094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap]
rs6426110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426114	0.95[ASN][1000 genomes]
rs6426115	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426117	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681790	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6685600	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691689	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696795	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699017	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73118046	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73128468	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73130436	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130448	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130455	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130462	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130464	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7522392	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7529143	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530205	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534101	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534447	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9287027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2405065	NVL	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224529200-224544000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:224535200-224536400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:224535200-224536600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr1:224535200-224536800	Enhancers	Primary T cells from cord blood	blood
5	chr1:224535200-224536800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:224535200-224536800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:224535200-224536800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:224535200-224536800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:224535400-224536800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:224535400-224536800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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