Variant report

Variant	rs12101540
Chromosome Location	chr15:73354551-73354552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73085797..73088021-chr15:73353697..73355855,2	MCF-7	breast:
2	chr15:73348449..73350291-chr15:73354149..73355949,2	MCF-7	breast:
3	chr15:73340283..73347207-chr15:73351084..73357651,9	MCF-7	breast:
4	chr15:73352462..73355061-chr15:73359053..73360956,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1017809	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1029	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1038136	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852881	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11853109	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856383	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856433	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856466	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11857053	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12101734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13329282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1382780	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1678245	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957661	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1714529	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1714530	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1714532	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1812363	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1842164	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1895842	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1963253	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1963254	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979410	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2169952	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254390	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2254818	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2623990	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2623994	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2623996	0.88[EUR][1000 genomes]
rs2680347	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2680348	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2680350	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2680351	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28547177	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28572029	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28582318	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28645758	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28676873	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28808999	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828370	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4238459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4287530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4325518	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4539561	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4635304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4776626	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4777584	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55969660	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57453823	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6495054	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176908	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7180017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438015	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7403367	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7497831	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031718	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8034243	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034826	0.93[AFR][1000 genomes]
rs8035499	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8035717	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038411	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs899480	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920152	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920459	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920675	0.94[AMR][1000 genomes];0.88[EUR][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	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73346400-73355000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:73346400-73355400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:73347000-73358800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:73348200-73355600	Weak transcription	Fetal Lung	lung
5	chr15:73348600-73355000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:73349200-73355000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:73349200-73355000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:73349400-73367000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:73351000-73355000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:73352000-73365000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:73353400-73354600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:73353400-73356800	Enhancers	Brain Hippocampus Middle	brain
13	chr15:73353600-73354600	Enhancers	Psoas Muscle	Psoas
14	chr15:73353600-73356400	Enhancers	Brain Angular Gyrus	brain
15	chr15:73353800-73363400	Weak transcription	Aorta	Aorta
16	chr15:73353800-73366000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:73353800-73367400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:73354000-73355000	Weak transcription	Brain Substantia Nigra	brain
19	chr15:73354000-73359000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:73354200-73354600	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr15:73354200-73354800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:73354400-73356000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr15:73354400-73356600	Enhancers	Brain Anterior Caudate	brain
24	chr15:73354400-73364800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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