Variant report

Variant	rs3789127
Chromosome Location	chr2:111704760-111704761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111695965..111698914-chr2:111704650..111707242,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10164695	0.83[CEU][hapmap]
rs10165663	0.84[CEU][hapmap]
rs10168046	0.83[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10169926	0.82[CEU][hapmap]
rs10171765	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs10175204	0.84[CEU][hapmap]
rs10177582	0.82[CEU][hapmap]
rs10180551	0.84[JPT][hapmap]
rs10184452	0.80[CEU][hapmap]
rs10185326	0.82[CEU][hapmap]
rs10186753	0.82[CEU][hapmap]
rs10188079	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs10188169	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs10193050	0.84[JPT][hapmap]
rs10197135	0.83[CEU][hapmap]
rs10197140	0.84[JPT][hapmap]
rs10202539	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204997	0.84[CEU][hapmap]
rs10208020	0.80[CEU][hapmap]
rs11123211	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs11123221	0.81[CEU][hapmap]
rs11123229	0.83[CEU][hapmap]
rs1114413	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114414	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11892748	0.84[JPT][hapmap]
rs11898005	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs12151613	0.84[JPT][hapmap]
rs12328918	0.84[CEU][hapmap]
rs12329097	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs12329216	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs12329344	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs12468564	0.84[JPT][hapmap]
rs12470827	0.84[CEU][hapmap]
rs12474757	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs12476335	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs12476386	0.80[CEU][hapmap]
rs12477660	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs13024140	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs13384044	0.82[CEU][hapmap]
rs13413838	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13424637	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs13426283	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs13429695	0.83[CEU][hapmap]
rs1513826	0.82[CEU][hapmap]
rs17465162	0.84[JPT][hapmap]
rs17465210	0.84[JPT][hapmap]
rs17466548	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs17466576	0.82[CEU][hapmap]
rs17525147	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs17545048	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs17545166	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs17545286	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs1872062	0.82[CEU][hapmap]
rs2128815	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2200211	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs2220092	0.84[JPT][hapmap]
rs2341897	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs2341913	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2880192	0.82[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs3761710	0.82[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs3789112	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3789114	0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3789116	0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3789121	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3789130	0.83[EUR][1000 genomes]
rs3789131	0.84[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs3827548	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4332932	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs4848344	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849120	0.84[JPT][hapmap]
rs4849162	0.83[CEU][hapmap]
rs4849164	0.82[CEU][hapmap]
rs4849165	0.82[CEU][hapmap]
rs4849170	0.84[CEU][hapmap]
rs4849201	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs4849203	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs4849298	0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62159558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542188	0.82[CEU][hapmap]
rs6542189	0.82[CEU][hapmap]
rs6542190	0.82[CEU][hapmap]
rs6720034	0.83[CEU][hapmap]
rs6720503	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs6737631	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs6751930	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs6758344	0.82[CEU][hapmap]
rs7355443	0.83[CEU][hapmap]
rs7355554	0.84[CEU][hapmap]
rs7569806	0.84[CEU][hapmap]
rs7609002	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs880506	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs900556	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs900557	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs9308691	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs9308692	0.82[CEU][hapmap]
rs932076	0.84[CEU][hapmap]
rs932078	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs999641	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1004949	chr2:111607532-111780719	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1002568	chr2:111607532-111781442	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1005665	chr2:111610107-111762039	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535892	chr2:111610107-111762039	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111693000-111706400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:111702000-111705200	Weak transcription	Thymus	Thymus
3	chr2:111704000-111706400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:111704200-111704800	Active TSS	Fetal Brain Male	brain
5	chr2:111704200-111705800	Enhancers	Lung	lung
6	chr2:111704200-111705800	Enhancers	Right Ventricle	heart
7	chr2:111704200-111706600	Enhancers	Fetal Heart	heart
8	chr2:111704200-111706800	Enhancers	Fetal Muscle Trunk	muscle
9	chr2:111704200-111706800	Enhancers	Left Ventricle	heart
10	chr2:111704200-111707000	Enhancers	Fetal Muscle Leg	muscle
11	chr2:111704200-111709600	Enhancers	Fetal Lung	lung
12	chr2:111704400-111704800	Enhancers	Colon Smooth Muscle	Colon
13	chr2:111704400-111704800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:111704400-111705000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:111704400-111705000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:111704400-111705200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:111704400-111705600	Enhancers	Primary B cells from cord blood	blood
18	chr2:111704400-111705600	Enhancers	Primary B cells from peripheral blood	blood
19	chr2:111704400-111705600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:111704400-111705600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:111704400-111705800	Enhancers	Psoas Muscle	Psoas
22	chr2:111704400-111706200	Enhancers	Adipose Nuclei	Adipose
23	chr2:111704600-111705000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:111704600-111706600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:111704600-111707000	Enhancers	Right Atrium	heart

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