Variant report

Variant	rs16945839
Chromosome Location	chr16:48160410-48160411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:48160028..48160849-chr16:48189962..48191269,4	MCF-7	breast:
2	chr16:48155501..48157445-chr16:48159306..48161176,2	MCF-7	breast:
3	chr16:47176198..47179127-chr16:48158467..48161279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171208	Chromatin interaction
ENSG00000260281	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11861448	1.00[EUR][1000 genomes]
rs11864016	1.00[EUR][1000 genomes]
rs11864570	1.00[EUR][1000 genomes]
rs12103132	1.00[EUR][1000 genomes]
rs13330281	1.00[EUR][1000 genomes]
rs13330882	1.00[EUR][1000 genomes]
rs13331266	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13333718	1.00[EUR][1000 genomes]
rs13334423	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13334475	1.00[EUR][1000 genomes]
rs13335010	1.00[EUR][1000 genomes]
rs1345425	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945786	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16945813	1.00[EUR][1000 genomes]
rs16945816	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945824	0.89[ASW][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945828	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945831	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945835	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945860	1.00[EUR][1000 genomes]
rs2016940	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28431782	1.00[EUR][1000 genomes]
rs28526661	1.00[EUR][1000 genomes]
rs28531369	1.00[EUR][1000 genomes]
rs28587611	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28592871	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28669266	1.00[EUR][1000 genomes]
rs34106426	1.00[EUR][1000 genomes]
rs4785405	1.00[EUR][1000 genomes]
rs56093600	1.00[EUR][1000 genomes]
rs57124014	1.00[EUR][1000 genomes]
rs57432729	1.00[EUR][1000 genomes]
rs57740199	1.00[EUR][1000 genomes]
rs58204235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58622309	1.00[EUR][1000 genomes]
rs59311846	1.00[EUR][1000 genomes]
rs59312258	1.00[EUR][1000 genomes]
rs59466391	1.00[EUR][1000 genomes]
rs59528776	1.00[EUR][1000 genomes]
rs59766379	1.00[EUR][1000 genomes]
rs59832329	1.00[EUR][1000 genomes]
rs59966196	1.00[EUR][1000 genomes]
rs6500304	1.00[EUR][1000 genomes]
rs6500305	1.00[EUR][1000 genomes]
rs7187069	1.00[EUR][1000 genomes]
rs7197701	1.00[EUR][1000 genomes]
rs7203314	1.00[EUR][1000 genomes]
rs73540833	1.00[EUR][1000 genomes]
rs73540845	1.00[EUR][1000 genomes]
rs73540853	1.00[EUR][1000 genomes]
rs74018249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74018255	1.00[EUR][1000 genomes]
rs8046592	1.00[EUR][1000 genomes]
rs8048367	1.00[EUR][1000 genomes]
rs8056553	1.00[EUR][1000 genomes]
rs8058288	1.00[EUR][1000 genomes]
rs9302750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs939360	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs939362	0.89[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs961668	1.00[EUR][1000 genomes]
rs9925287	1.00[EUR][1000 genomes]
rs9926338	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9933094	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9933277	1.00[EUR][1000 genomes]
rs9935027	1.00[EUR][1000 genomes]
rs9936500	1.00[EUR][1000 genomes]
rs9936532	1.00[EUR][1000 genomes]
rs9938810	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9940987	0.89[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[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	nsv520355	chr16:47424828-48164777	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48146400-48160600	Weak transcription	Right Atrium	heart
2	chr16:48147600-48160600	Weak transcription	Psoas Muscle	Psoas
3	chr16:48152200-48160600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:48153600-48160600	Weak transcription	Pancreas	Pancrea
5	chr16:48155200-48163200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr16:48156400-48163000	Enhancers	NH-A	brain
7	chr16:48156400-48163200	Enhancers	HSMM	muscle
8	chr16:48156400-48163400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:48157600-48160600	Weak transcription	Hela-S3	cervix
10	chr16:48157600-48160800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:48157800-48160800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr16:48158000-48160600	Weak transcription	HUVEC	blood vessel
13	chr16:48158000-48160800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr16:48158000-48161200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr16:48158200-48160600	Weak transcription	NHEK	skin
16	chr16:48158200-48160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:48158200-48161800	Enhancers	Left Ventricle	heart
18	chr16:48158600-48160600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr16:48158600-48161200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:48158600-48161200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr16:48159000-48160600	Weak transcription	HMEC	breast
22	chr16:48159000-48162600	Enhancers	Fetal Muscle Leg	muscle
23	chr16:48159000-48164000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr16:48159200-48161400	Enhancers	Adipose Nuclei	Adipose
25	chr16:48159200-48161600	Enhancers	Right Ventricle	heart
26	chr16:48159400-48160600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:48159400-48160600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr16:48159400-48160800	Enhancers	Fetal Lung	lung
29	chr16:48159400-48161800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr16:48159600-48160600	Weak transcription	Lung	lung
31	chr16:48159600-48160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr16:48159800-48160600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr16:48159800-48163200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:48159800-48164000	Enhancers	Osteobl	bone
35	chr16:48160200-48160600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr16:48160200-48161600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr16:48160200-48161600	Enhancers	Fetal Muscle Trunk	muscle
38	chr16:48160200-48163000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr16:48160200-48163400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr16:48160400-48161000	Flanking Active TSS	A549	lung
41	chr16:48160400-48161600	Enhancers	Stomach Mucosa	stomach
42	chr16:48160400-48163000	Enhancers	NHLF	lung
43	chr16:48160400-48163400	Enhancers	HSMMtube	muscle
44	chr16:48160400-48163400	Enhancers	NHDF-Ad	bronchial

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