Variant report

Variant	rs1404872
Chromosome Location	chr7:3344986-3344987
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	chr7:3340838..3343187-chr7:3343470..3345833,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236708	Chromatin interaction
ENSG00000146555	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs11972733	1.00[ASN][1000 genomes]
rs11973104	1.00[ASN][1000 genomes]
rs11973436	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973741	1.00[ASN][1000 genomes]
rs11973959	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974237	0.82[CEU][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974565	0.82[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975560	0.86[EUR][1000 genomes]
rs11975595	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978310	1.00[ASN][1000 genomes]
rs11979270	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981004	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981125	1.00[ASN][1000 genomes]
rs11981207	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981998	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982674	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983024	0.86[YRI][hapmap]
rs11983341	1.00[ASN][1000 genomes]
rs12700786	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700790	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700791	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236105	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522503	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133260	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133277	0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133284	1.00[ASN][1000 genomes]
rs17133303	1.00[GIH][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs17133309	1.00[ASN][1000 genomes]
rs17133324	0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs17133377	0.89[TSI][hapmap]
rs17741019	1.00[ASN][1000 genomes]
rs2334059	0.81[EUR][1000 genomes]
rs34431029	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34466031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34727194	1.00[ASN][1000 genomes]
rs35298757	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268017	0.82[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4358699	1.00[ASN][1000 genomes]
rs4428572	1.00[ASN][1000 genomes]
rs4509207	0.82[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560699	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55944002	1.00[ASN][1000 genomes]
rs56064609	0.81[EUR][1000 genomes]
rs56138263	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56193850	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56217543	1.00[ASN][1000 genomes]
rs57534358	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57535226	0.86[EUR][1000 genomes]
rs57585396	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58338081	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59021191	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59076306	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59296189	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59478367	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59673826	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60243572	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60418263	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60682391	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61039995	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61401313	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492969	1.00[ASN][1000 genomes]
rs66546301	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66665337	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66790405	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66941572	1.00[ASN][1000 genomes]
rs67447866	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67498702	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67637487	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67691723	1.00[ASN][1000 genomes]
rs67924867	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68115111	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68165343	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942774	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943523	0.86[EUR][1000 genomes]
rs6944617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944745	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945914	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946840	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948557	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952184	1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955021	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959134	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959489	1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs6962043	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963043	1.00[ASN][1000 genomes]
rs6964818	0.86[EUR][1000 genomes]
rs6969044	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969455	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969711	0.92[GIH][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs6974121	1.00[ASN][1000 genomes]
rs6977110	1.00[ASN][1000 genomes]
rs6977532	0.84[EUR][1000 genomes]
rs73034713	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034779	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036706	1.00[ASN][1000 genomes]
rs73045613	0.82[EUR][1000 genomes]
rs73045637	0.82[EUR][1000 genomes]
rs73045677	0.86[EUR][1000 genomes]
rs73046618	0.95[EUR][1000 genomes]
rs73046656	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046658	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046661	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046682	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046689	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046694	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046699	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046702	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048614	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048617	0.86[EUR][1000 genomes]
rs73048621	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048624	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048628	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048630	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048631	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048634	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048643	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048645	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048648	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048655	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048661	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048672	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048676	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048677	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048700	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73049436	0.82[EUR][1000 genomes]
rs73049438	0.82[EUR][1000 genomes]
rs73050503	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050538	1.00[ASN][1000 genomes]
rs73050542	1.00[ASN][1000 genomes]
rs73052642	1.00[ASN][1000 genomes]
rs7779193	0.82[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782339	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783541	0.84[EUR][1000 genomes]
rs7785207	0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792929	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807563	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808804	0.82[EUR][1000 genomes]
rs9771086	1.00[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3342600-3347200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:3342800-3345000	Weak transcription	Adipose Nuclei	Adipose
3	chr7:3343000-3345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:3343800-3357000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:3344000-3347000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:3344200-3345200	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:3344600-3345200	Enhancers	Fetal Brain Male	brain
8	chr7:3344600-3345400	Weak transcription	Aorta	Aorta
9	chr7:3344600-3366600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:3344800-3354600	Weak transcription	Pancreas	Pancrea

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