Variant report

Variant	rs1545196
Chromosome Location	chr2:64282310-64282311
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64282144..64283036-chr2:64539270..64540071,2	MCF-7	breast:
2	chr2:64275467..64277323-chr2:64280220..64283208,2	MCF-7	breast:
3	chr2:64280836..64282865-chr2:64492384..64494313,2	MCF-7	breast:
4	chr2:64275419..64277085-chr2:64280616..64282779,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10166971	0.84[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs10190776	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12463827	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12466966	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12468093	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472816	1.00[CHB][hapmap]
rs12475294	0.86[EUR][1000 genomes]
rs12477310	0.89[CHB][hapmap]
rs12479211	1.00[CHB][hapmap]
rs12990604	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12993544	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12996147	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997303	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999675	0.85[EUR][1000 genomes]
rs13005218	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13007342	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13007731	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13009774	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13010817	0.83[EUR][1000 genomes]
rs13014781	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13015703	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023542	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13025640	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028805	0.80[EUR][1000 genomes]
rs13034260	0.85[EUR][1000 genomes]
rs1345479	0.85[EUR][1000 genomes]
rs1437455	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17555655	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17562312	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17620012	0.85[EUR][1000 genomes]
rs17701685	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17701709	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17752683	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002443	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287361	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2422110	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2422111	0.84[AMR][1000 genomes]
rs34043307	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34145077	0.85[EUR][1000 genomes]
rs34200806	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34512058	0.85[EUR][1000 genomes]
rs34683043	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34700615	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35122209	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35247801	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35521527	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35648996	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35693031	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35810427	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35939512	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35972278	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35975566	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815616	0.85[EUR][1000 genomes]
rs3934536	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4482470	0.85[EUR][1000 genomes]
rs4485552	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4544421	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4599090	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4671072	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4671537	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671538	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671540	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671541	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66476638	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66535980	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66595136	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66650505	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66660401	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66993685	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67366434	0.80[EUR][1000 genomes]
rs6759803	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67962955	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71422402	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72808231	0.86[EUR][1000 genomes]
rs72808248	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72808254	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72808262	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72808287	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72808296	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7349403	1.00[CHB][hapmap]
rs874695	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893779	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64277400-64282600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:64277400-64291200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:64278600-64282600	Enhancers	Primary T cells from cord blood	blood
4	chr2:64278600-64285400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:64278800-64283400	Enhancers	Fetal Thymus	thymus
6	chr2:64279000-64282600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr2:64279000-64282800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr2:64279000-64282800	Enhancers	Thymus	Thymus
9	chr2:64279600-64285400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:64279800-64282400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:64279800-64282600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:64279800-64282600	Weak transcription	Placenta	Placenta
13	chr2:64280000-64283200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:64280000-64283200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:64280000-64285400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:64280000-64290600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:64281200-64283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:64281400-64284400	Enhancers	HMEC	breast
19	chr2:64281600-64282400	Enhancers	GM12878-XiMat	blood
20	chr2:64281600-64290800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:64281600-64291200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:64281800-64282400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:64282000-64284200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:64282000-64284400	Enhancers	NHEK	skin
25	chr2:64282000-64290200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:64282000-64290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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