Variant report

Variant	rs10888569
Chromosome Location	chr1:150025672-150025673
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	chr1:149858020..149860517-chr1:150024579..150026129,2	MCF-7	breast:
2	chr1:149858594..149860168-chr1:150024352..150026596,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10494264	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10749674	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10888568	0.97[EUR][1000 genomes]
rs10888572	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1105209	0.81[EUR][1000 genomes]
rs11205316	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11205317	0.96[EUR][1000 genomes]
rs11205319	0.96[EUR][1000 genomes]
rs11205321	0.98[EUR][1000 genomes]
rs11205326	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11205329	0.87[EUR][1000 genomes]
rs11205331	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11205333	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11205337	0.80[EUR][1000 genomes]
rs11577346	0.90[EUR][1000 genomes]
rs11583720	0.94[EUR][1000 genomes]
rs11584091	0.90[EUR][1000 genomes]
rs11584354	0.95[EUR][1000 genomes]
rs11585955	0.94[EUR][1000 genomes]
rs11587963	0.90[EUR][1000 genomes]
rs11589585	0.96[EUR][1000 genomes]
rs11589801	0.83[EUR][1000 genomes]
rs11589922	0.85[EUR][1000 genomes]
rs11591200	0.85[EUR][1000 genomes]
rs12058090	0.96[EUR][1000 genomes]
rs12058502	0.95[EUR][1000 genomes]
rs12060027	0.97[EUR][1000 genomes]
rs12060211	0.96[EUR][1000 genomes]
rs12061167	0.96[EUR][1000 genomes]
rs12061196	0.96[EUR][1000 genomes]
rs12061565	0.96[EUR][1000 genomes]
rs12061856	0.96[EUR][1000 genomes]
rs12062861	0.95[EUR][1000 genomes]
rs12063059	0.96[EUR][1000 genomes]
rs12063281	0.95[EUR][1000 genomes]
rs12063329	0.95[EUR][1000 genomes]
rs12064532	0.92[EUR][1000 genomes]
rs12065681	0.96[EUR][1000 genomes]
rs12066132	0.96[EUR][1000 genomes]
rs12066293	0.96[EUR][1000 genomes]
rs12067422	0.96[EUR][1000 genomes]
rs12073359	0.96[EUR][1000 genomes]
rs12074281	0.98[EUR][1000 genomes]
rs12093499	0.95[EUR][1000 genomes]
rs12098106	0.96[EUR][1000 genomes]
rs12124898	0.81[EUR][1000 genomes]
rs12138231	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12139248	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1339494	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1339495	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1382573	0.85[EUR][1000 genomes]
rs1545762	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1824847	0.90[AFR][1000 genomes]
rs1824848	0.84[EUR][1000 genomes]
rs1824849	0.85[EUR][1000 genomes]
rs1824850	0.85[EUR][1000 genomes]
rs1964542	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1975957	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2027349	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2039800	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2169895	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2318763	0.90[EUR][1000 genomes]
rs2319280	0.96[EUR][1000 genomes]
rs28366567	0.94[EUR][1000 genomes]
rs28443768	0.96[EUR][1000 genomes]
rs28560140	0.96[EUR][1000 genomes]
rs28660389	0.97[EUR][1000 genomes]
rs28753817	0.96[EUR][1000 genomes]
rs3208509	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3850838	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3925724	0.92[EUR][1000 genomes]
rs4058847	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4926388	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4926391	0.84[EUR][1000 genomes]
rs4926406	0.85[EUR][1000 genomes]
rs4926407	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4926408	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4926409	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4926411	0.83[EUR][1000 genomes]
rs4926412	0.83[EUR][1000 genomes]
rs55633125	0.96[EUR][1000 genomes]
rs55647342	0.99[EUR][1000 genomes]
rs55802315	0.85[EUR][1000 genomes]
rs55840680	0.90[EUR][1000 genomes]
rs55840906	0.95[EUR][1000 genomes]
rs55909733	0.90[EUR][1000 genomes]
rs55918911	0.97[EUR][1000 genomes]
rs56125600	0.97[EUR][1000 genomes]
rs56188926	0.93[EUR][1000 genomes]
rs56212907	0.93[EUR][1000 genomes]
rs56349882	0.85[EUR][1000 genomes]
rs56369603	0.90[EUR][1000 genomes]
rs57926929	0.91[EUR][1000 genomes]
rs58426216	0.88[EUR][1000 genomes]
rs59607464	0.85[EUR][1000 genomes]
rs6657062	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6666959	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6687454	0.95[EUR][1000 genomes]
rs6694729	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72692857	0.95[EUR][1000 genomes]
rs72692861	0.96[EUR][1000 genomes]
rs72692862	0.95[EUR][1000 genomes]
rs72692865	0.96[EUR][1000 genomes]
rs72692866	0.96[EUR][1000 genomes]
rs72692869	0.96[EUR][1000 genomes]
rs72692886	0.95[EUR][1000 genomes]
rs72692893	0.93[EUR][1000 genomes]
rs72692895	0.94[EUR][1000 genomes]
rs72692896	0.94[EUR][1000 genomes]
rs72692897	0.94[EUR][1000 genomes]
rs72692898	0.93[EUR][1000 genomes]
rs72692899	0.93[EUR][1000 genomes]
rs72692900	0.93[EUR][1000 genomes]
rs72692901	0.94[EUR][1000 genomes]
rs72694905	0.91[EUR][1000 genomes]
rs72694906	0.93[EUR][1000 genomes]
rs72694908	0.93[EUR][1000 genomes]
rs72694914	0.92[EUR][1000 genomes]
rs72694915	0.92[EUR][1000 genomes]
rs72694917	0.93[EUR][1000 genomes]
rs72694918	0.93[EUR][1000 genomes]
rs72694919	0.93[EUR][1000 genomes]
rs72694923	0.92[EUR][1000 genomes]
rs72694926	0.90[EUR][1000 genomes]
rs72694927	0.91[EUR][1000 genomes]
rs72694928	0.90[EUR][1000 genomes]
rs72694933	0.90[EUR][1000 genomes]
rs72694936	0.90[EUR][1000 genomes]
rs72694942	0.90[EUR][1000 genomes]
rs72694943	0.91[EUR][1000 genomes]
rs72694944	0.90[EUR][1000 genomes]
rs72694945	0.90[EUR][1000 genomes]
rs72694946	0.90[EUR][1000 genomes]
rs72694950	0.90[EUR][1000 genomes]
rs72694951	0.90[EUR][1000 genomes]
rs72694953	0.90[EUR][1000 genomes]
rs72694954	0.89[EUR][1000 genomes]
rs72694956	0.85[EUR][1000 genomes]
rs72694957	0.85[EUR][1000 genomes]
rs72694959	0.85[EUR][1000 genomes]
rs72694962	0.81[EUR][1000 genomes]
rs7519918	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7520930	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7521768	0.82[EUR][1000 genomes]
rs7521783	0.82[EUR][1000 genomes]
rs7530922	0.96[EUR][1000 genomes]
rs7540847	0.98[EUR][1000 genomes]
rs7550323	0.98[EUR][1000 genomes]
rs7550350	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7553622	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7554367	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7555080	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9662055	0.96[EUR][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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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 target site	431 gene(s)	inside rSNPs	diseases
2	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv947321	chr1:150007387-150030042	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 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	chr1:149996600-150037000	Weak transcription	Left Ventricle	heart
2	chr1:150017600-150026200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:150017600-150037600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:150017800-150025800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:150017800-150026000	Weak transcription	Osteobl	bone
6	chr1:150018000-150031600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:150018000-150033400	Weak transcription	Fetal Stomach	stomach
8	chr1:150018200-150038600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:150022200-150025800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:150022800-150025800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:150022800-150025800	Weak transcription	GM12878-XiMat	blood
12	chr1:150022800-150032400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:150022800-150037200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:150022800-150038600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:150023000-150025800	Weak transcription	Adipose Nuclei	Adipose
16	chr1:150023000-150026000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:150023000-150028600	Weak transcription	Primary B cells from cord blood	blood
18	chr1:150023000-150033600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:150024200-150026000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:150024400-150025800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:150024400-150026000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:150024400-150026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:150025200-150027200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:150025400-150025800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr1:150025400-150026600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:150025600-150026000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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