Variant report

Variant	rs12902212
Chromosome Location	chr15:45495229-45495230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45494024..45495941-chr15:45555811..45558017,2	MCF-7	breast:
2	chr15:45493253..45495607-chr15:45694426..45696533,2	K562	blood:
3	chr15:45494998..45498237-chr15:45508390..45511192,3	K562	blood:
4	chr15:45453899..45457914-chr15:45495194..45498173,3	K562	blood:
5	chr15:45491434..45494359-chr15:45494448..45497644,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138606	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000171763	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10450969	0.89[EUR][1000 genomes]
rs10450970	0.91[EUR][1000 genomes]
rs10467979	0.93[EUR][1000 genomes]
rs10775129	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851421	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851422	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851423	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070444	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070451	0.92[EUR][1000 genomes]
rs11634794	0.92[EUR][1000 genomes]
rs11636018	0.92[EUR][1000 genomes]
rs11636410	0.91[EUR][1000 genomes]
rs11636440	0.91[EUR][1000 genomes]
rs11639403	0.92[EUR][1000 genomes]
rs11854234	0.89[EUR][1000 genomes]
rs11854294	0.92[EUR][1000 genomes]
rs11854345	0.90[EUR][1000 genomes]
rs11854347	0.92[EUR][1000 genomes]
rs11854377	0.92[EUR][1000 genomes]
rs11854689	0.93[EUR][1000 genomes]
rs11854690	0.93[EUR][1000 genomes]
rs11855435	0.88[EUR][1000 genomes]
rs11855466	0.92[EUR][1000 genomes]
rs11857919	0.92[EUR][1000 genomes]
rs11858988	0.86[EUR][1000 genomes]
rs12323957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437603	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440238	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440321	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440793	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592055	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593605	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901114	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903149	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904079	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904265	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904331	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12904591	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12904815	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12905053	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12905246	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906537	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906734	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909987	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910214	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910270	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910357	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910591	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911551	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913123	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12915027	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915804	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915965	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917187	0.92[EUR][1000 genomes]
rs13329225	0.92[EUR][1000 genomes]
rs13329228	0.92[EUR][1000 genomes]
rs1631533	0.93[EUR][1000 genomes]
rs1648285	0.93[EUR][1000 genomes]
rs1648286	0.93[EUR][1000 genomes]
rs1648287	0.93[EUR][1000 genomes]
rs1648289	0.93[EUR][1000 genomes]
rs1648295	0.92[EUR][1000 genomes]
rs1648302	0.98[EUR][1000 genomes]
rs16941017	0.91[EUR][1000 genomes]
rs1706763	0.90[EUR][1000 genomes]
rs1706764	0.93[EUR][1000 genomes]
rs1706821	0.80[EUR][1000 genomes]
rs1706822	0.80[EUR][1000 genomes]
rs1706832	0.93[EUR][1000 genomes]
rs1706834	0.93[EUR][1000 genomes]
rs1706835	0.93[EUR][1000 genomes]
rs1706837	0.93[EUR][1000 genomes]
rs2413775	0.90[EUR][1000 genomes]
rs2413776	0.91[EUR][1000 genomes]
rs2413778	0.92[EUR][1000 genomes]
rs2413780	0.92[EUR][1000 genomes]
rs2413782	0.92[EUR][1000 genomes]
rs2413786	0.93[EUR][1000 genomes]
rs2433227	0.93[EUR][1000 genomes]
rs2433228	0.93[EUR][1000 genomes]
rs2433229	0.93[EUR][1000 genomes]
rs2458224	0.93[EUR][1000 genomes]
rs2467838	0.83[EUR][1000 genomes]
rs2554453	0.90[EUR][1000 genomes]
rs2554454	0.93[EUR][1000 genomes]
rs2554455	0.93[EUR][1000 genomes]
rs2554456	0.93[EUR][1000 genomes]
rs2554457	0.93[EUR][1000 genomes]
rs2668737	0.93[EUR][1000 genomes]
rs2668751	0.93[EUR][1000 genomes]
rs28498330	0.82[EUR][1000 genomes]
rs28524974	0.91[EUR][1000 genomes]
rs28526629	0.92[EUR][1000 genomes]
rs28628668	0.90[EUR][1000 genomes]
rs28680861	0.83[EUR][1000 genomes]
rs28701495	0.81[EUR][1000 genomes]
rs28733848	0.93[EUR][1000 genomes]
rs28756676	0.92[EUR][1000 genomes]
rs28789819	0.92[EUR][1000 genomes]
rs28815867	0.92[EUR][1000 genomes]
rs28847337	0.85[EUR][1000 genomes]
rs28851791	0.92[EUR][1000 genomes]
rs28859291	0.92[EUR][1000 genomes]
rs28877685	0.92[EUR][1000 genomes]
rs28889270	0.92[EUR][1000 genomes]
rs28897155	0.92[EUR][1000 genomes]
rs28897234	0.88[EUR][1000 genomes]
rs2899378	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899379	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759892	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759893	0.91[EUR][1000 genomes]
rs3759895	0.91[EUR][1000 genomes]
rs3959644	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3985919	0.93[EUR][1000 genomes]
rs4238376	0.92[EUR][1000 genomes]
rs4238377	0.89[EUR][1000 genomes]
rs4270107	0.89[EUR][1000 genomes]
rs4439707	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4442750	0.89[EUR][1000 genomes]
rs4444275	0.89[EUR][1000 genomes]
rs4514617	0.92[EUR][1000 genomes]
rs4544188	0.91[EUR][1000 genomes]
rs4774542	0.93[EUR][1000 genomes]
rs4774550	0.92[EUR][1000 genomes]
rs4775819	0.93[EUR][1000 genomes]
rs4775822	0.92[EUR][1000 genomes]
rs4775823	0.92[EUR][1000 genomes]
rs4775826	0.92[EUR][1000 genomes]
rs4775831	0.91[EUR][1000 genomes]
rs4775832	0.91[EUR][1000 genomes]
rs4775834	0.92[EUR][1000 genomes]
rs4775835	0.92[EUR][1000 genomes]
rs4775836	0.92[EUR][1000 genomes]
rs4775837	0.92[EUR][1000 genomes]
rs4775844	0.92[EUR][1000 genomes]
rs55771002	0.92[EUR][1000 genomes]
rs55920042	0.92[EUR][1000 genomes]
rs62026661	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62026665	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62026666	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7167326	0.88[EUR][1000 genomes]
rs7167731	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169015	0.91[EUR][1000 genomes]
rs7171401	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174913	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45493400-45495400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:45493400-45495400	Weak transcription	Ovary	ovary
3	chr15:45493400-45497000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:45493600-45495400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:45493600-45495400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:45493600-45495400	Weak transcription	Left Ventricle	heart
7	chr15:45493600-45496000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr15:45493600-45497000	Weak transcription	HSMMtube	muscle
9	chr15:45493600-45497200	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:45493600-45508000	Weak transcription	Right Atrium	heart
11	chr15:45493800-45495600	Weak transcription	Adipose Nuclei	Adipose
12	chr15:45493800-45497000	Weak transcription	Stomach Mucosa	stomach
13	chr15:45494000-45495600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr15:45494000-45496200	Enhancers	Liver	Liver
15	chr15:45494000-45497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:45494000-45497000	Weak transcription	Fetal Intestine Small	intestine
17	chr15:45494000-45497200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:45494000-45497200	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:45494000-45497200	Weak transcription	Fetal Intestine Large	intestine
20	chr15:45494200-45495400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:45494200-45495400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:45494200-45495800	Enhancers	GM12878-XiMat	blood
23	chr15:45494200-45496800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:45494400-45495400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:45494400-45495400	Enhancers	HepG2	liver
26	chr15:45494600-45495600	Enhancers	Brain Substantia Nigra	brain
27	chr15:45495000-45496000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:45495000-45496200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:45495200-45495600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr15:45495200-45496400	Enhancers	Osteobl	bone

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