Variant report

Variant	rs2733221
Chromosome Location	chr15:44389870-44389871
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	chr15:44371231..44374212-chr15:44389426..44392259,2	MCF-7	breast:

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10152607	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10459588	1.00[CEU][hapmap]
rs10518994	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10851415	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10851416	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070419	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1115870	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1160066	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11631340	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11632901	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11635948	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11638352	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11854312	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11857696	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12324261	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12437804	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs12591537	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12900237	1.00[CEU][hapmap]
rs12900880	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12913809	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1365456	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1426657	1.00[CEU][hapmap]
rs1426658	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs1808509	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1813196	0.87[AFR][1000 genomes]
rs1820482	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs1820484	0.83[AFR][1000 genomes]
rs1834641	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2015277	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2019074	0.91[EUR][1000 genomes]
rs2042738	1.00[CEU][hapmap]
rs2042739	1.00[CEU][hapmap]
rs2042741	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2059626	0.91[EUR][1000 genomes]
rs2059627	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2059628	0.91[EUR][1000 genomes]
rs2114416	0.83[AFR][1000 genomes]
rs2114420	0.94[EUR][1000 genomes]
rs2114421	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2114422	1.00[CEU][hapmap]
rs2162365	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2162366	1.00[CEU][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs2217108	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2412845	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412846	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412847	0.97[EUR][1000 genomes]
rs2412848	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412849	1.00[CEU][hapmap]
rs2412850	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2412851	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412852	0.94[EUR][1000 genomes]
rs2412853	0.81[ASW][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412854	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412855	0.94[EUR][1000 genomes]
rs2447334	0.84[GIH][hapmap]
rs2555375	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2555376	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap]
rs2555380	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2555384	1.00[CEU][hapmap]
rs2555385	0.91[EUR][1000 genomes]
rs2555387	1.00[CEU][hapmap]
rs2555389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2615268	0.80[AFR][1000 genomes]
rs2615272	0.81[AFR][1000 genomes]
rs2615278	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs2615281	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs2615285	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2615287	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2615288	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2615290	0.91[EUR][1000 genomes]
rs2615291	0.88[EUR][1000 genomes]
rs2615292	0.91[EUR][1000 genomes]
rs2615293	1.00[CEU][hapmap]
rs2615294	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2615295	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2615297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2615299	1.00[CEU][hapmap]
rs2615300	0.84[GIH][hapmap]
rs2623017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2623019	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2696074	0.84[GIH][hapmap]
rs2696094	1.00[CEU][hapmap]
rs2696098	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs2706471	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2706472	1.00[CEU][hapmap]
rs2706473	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2706474	0.91[EUR][1000 genomes]
rs2706481	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2706486	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs2706487	1.00[CEU][hapmap];0.83[AFR][1000 genomes]
rs2706488	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2706490	1.00[CEU][hapmap]
rs2706495	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap]
rs2733201	0.88[AFR][1000 genomes]
rs2733203	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2733204	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2733208	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs2733209	1.00[CEU][hapmap]
rs2733213	1.00[CEU][hapmap]
rs2733226	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs28667396	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2899103	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2929275	0.84[GIH][hapmap]
rs2929281	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930528	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2957581	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2957583	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3919618	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4419034	0.94[EUR][1000 genomes]
rs481837	0.82[TSI][hapmap]
rs4923969	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923976	1.00[CEU][hapmap]
rs4924727	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4924728	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4924729	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924731	0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924734	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924735	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924737	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493092	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493093	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493094	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs7166715	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7176955	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8033233	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8035212	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8035382	0.92[GIH][hapmap]
rs8035402	0.92[GIH][hapmap]
rs8036541	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8037441	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8037596	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8038096	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs8041487	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8041650	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs890465	1.00[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs958485	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9920249	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
3	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1052511	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv542371	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1045362	chr15:44280481-44414443	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv832989	chr15:44306469-44461710	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3351630	chr15:44334624-44547841	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv94497	chr15:44385556-44390318	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv977868	chr15:44389139-44392712	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2733221	LOC440278	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44373600-44392800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:44379400-44397400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:44381200-44394200	Weak transcription	HUVEC	blood vessel
4	chr15:44381800-44400800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:44384600-44393400	Weak transcription	HSMMtube	muscle
6	chr15:44384800-44391800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:44384800-44393400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:44385000-44391400	Weak transcription	NHLF	lung
9	chr15:44385000-44392800	Weak transcription	HMEC	breast
10	chr15:44385000-44393400	Weak transcription	A549	lung
11	chr15:44385000-44393400	Weak transcription	HSMM	muscle
12	chr15:44385000-44393600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:44385000-44393600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:44385800-44393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:44386800-44391800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:44387400-44391200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:44387400-44392800	Weak transcription	Osteobl	bone
18	chr15:44387600-44390200	Enhancers	Brain Cingulate Gyrus	brain
19	chr15:44387800-44391400	Weak transcription	NH-A	brain
20	chr15:44388000-44393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:44388200-44390000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr15:44388600-44398000	Enhancers	Brain Substantia Nigra	brain
23	chr15:44388800-44390000	Enhancers	Brain Angular Gyrus	brain
24	chr15:44388800-44390000	Enhancers	Fetal Heart	heart
25	chr15:44388800-44390200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:44388800-44391800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr15:44389000-44390200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:44389000-44390200	Enhancers	Brain Anterior Caudate	brain
29	chr15:44389200-44391400	Weak transcription	NHDF-Ad	bronchial
30	chr15:44389400-44390200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:44389600-44390200	Enhancers	Liver	Liver
32	chr15:44389800-44390000	Enhancers	Brain Hippocampus Middle	brain
33	chr15:44389800-44390400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr15:44389800-44391800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:44389800-44392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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