Variant report

Variant	rs28676873
Chromosome Location	chr15:73374695-73374696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73088811..73089611-chr15:73374330..73375082,2	MCF-7	breast:
2	chr15:73074981..73077571-chr15:73371548..73374920,3	MCF-7	breast:
3	chr15:73087557..73089460-chr15:73373408..73375516,2	MCF-7	breast:
4	chr15:73344322..73346287-chr15:73373187..73375620,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159322	Chromatin interaction
ENSG00000260898	Chromatin interaction
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1017809	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1029	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1038136	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852881	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11853109	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856383	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856466	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11857053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12101540	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12101734	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13329282	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1382780	0.88[EUR][1000 genomes]
rs1648248	0.82[EUR][1000 genomes]
rs1678245	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957661	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1714529	0.88[EUR][1000 genomes]
rs1714530	0.88[EUR][1000 genomes]
rs1714532	0.88[EUR][1000 genomes]
rs1812363	0.88[EUR][1000 genomes]
rs1842164	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1895842	0.82[EUR][1000 genomes]
rs1963253	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1963254	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979410	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2169952	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254390	0.85[EUR][1000 genomes]
rs2254818	0.85[EUR][1000 genomes]
rs2623990	0.85[EUR][1000 genomes]
rs2623994	0.82[EUR][1000 genomes]
rs2623996	0.88[EUR][1000 genomes]
rs2680347	0.88[EUR][1000 genomes]
rs2680348	0.82[EUR][1000 genomes]
rs2680350	0.82[EUR][1000 genomes]
rs2680351	0.88[EUR][1000 genomes]
rs28547177	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28572029	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28582318	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28645758	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28808999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4238459	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4287530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4325518	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4539561	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4635304	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4776626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4777584	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs533460	0.82[EUR][1000 genomes]
rs55969660	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57453823	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6495054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176908	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7180017	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438015	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7403367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7497831	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8034243	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034826	0.95[AFR][1000 genomes]
rs8035499	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8035717	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038411	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs899480	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920152	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920459	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920675	0.89[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73368200-73375600	Enhancers	Brain Substantia Nigra	brain
2	chr15:73368200-73381000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:73368600-73375200	Weak transcription	Aorta	Aorta
4	chr15:73370200-73375600	Enhancers	Stomach Mucosa	stomach
5	chr15:73371000-73375200	Weak transcription	Gastric	stomach
6	chr15:73371000-73376600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:73371200-73376800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:73371200-73388600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:73371200-73397000	Weak transcription	Pancreas	Pancrea
10	chr15:73371400-73375200	Weak transcription	A549	lung
11	chr15:73371600-73377400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:73371600-73393800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:73371800-73375000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:73371800-73375200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:73372200-73375200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:73372400-73375000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:73372400-73375200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr15:73372600-73375000	Weak transcription	Liver	Liver
19	chr15:73372600-73375200	Weak transcription	Fetal Lung	lung
20	chr15:73372600-73375400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:73372800-73375200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:73373200-73375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:73373200-73375000	Weak transcription	Brain Anterior Caudate	brain
24	chr15:73373200-73375200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:73373200-73375200	Weak transcription	Psoas Muscle	Psoas
26	chr15:73373200-73375400	Weak transcription	Small Intestine	intestine
27	chr15:73373800-73375000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:73373800-73376200	Enhancers	Fetal Intestine Large	intestine
29	chr15:73374000-73375200	Weak transcription	Brain Angular Gyrus	brain
30	chr15:73374000-73376000	Enhancers	Duodenum Mucosa	Duodenum
31	chr15:73374200-73375200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:73374200-73375200	Weak transcription	Fetal Kidney	kidney
33	chr15:73374200-73393600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:73374400-73374800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:73374600-73375000	Weak transcription	Fetal Intestine Small	intestine
36	chr15:73374600-73375200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:73374600-73375800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr15:73374600-73376200	Enhancers	Pancreatic Islets	Pancreatic Islet

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