Variant report

Variant	rs16887928
Chromosome Location	chr6:56317078-56317079
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	chr6:56303405..56305333-chr6:56316086..56317917,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1024196	0.89[EUR][1000 genomes]
rs11963288	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11966986	0.89[EUR][1000 genomes]
rs11967796	0.89[EUR][1000 genomes]
rs11970410	0.89[EUR][1000 genomes]
rs1407831	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535609	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1535611	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16888070	0.89[EUR][1000 genomes]
rs16888106	0.89[EUR][1000 genomes]
rs2144407	0.89[EUR][1000 genomes]
rs2180148	0.89[EUR][1000 genomes]
rs2207678	0.89[EUR][1000 genomes]
rs2397224	1.00[EUR][1000 genomes]
rs28633631	0.89[EUR][1000 genomes]
rs3800026	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3924307	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41267673	0.89[EUR][1000 genomes]
rs41271848	1.00[EUR][1000 genomes]
rs41271850	1.00[EUR][1000 genomes]
rs41271854	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41271856	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41271872	0.89[EUR][1000 genomes]
rs41271876	0.89[EUR][1000 genomes]
rs41271878	0.89[EUR][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4288197	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs45442999	0.94[EUR][1000 genomes]
rs45553042	0.84[EUR][1000 genomes]
rs57289287	0.89[EUR][1000 genomes]
rs57350484	0.89[EUR][1000 genomes]
rs57790896	0.89[EUR][1000 genomes]
rs57822928	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58730144	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59772940	0.89[EUR][1000 genomes]
rs59864125	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459167	0.89[EUR][1000 genomes]
rs6900572	0.89[EUR][1000 genomes]
rs6903815	0.89[EUR][1000 genomes]
rs6941626	0.89[EUR][1000 genomes]
rs73455767	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73455782	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73465854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73746926	0.89[EUR][1000 genomes]
rs73747826	1.00[EUR][1000 genomes]
rs73747832	1.00[EUR][1000 genomes]
rs73749935	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749942	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749948	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749949	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7749100	0.89[EUR][1000 genomes]
rs7759479	0.89[EUR][1000 genomes]
rs7760503	0.89[EUR][1000 genomes]
rs7760515	0.89[EUR][1000 genomes]
rs7760542	0.89[EUR][1000 genomes]
rs7760701	0.89[EUR][1000 genomes]
rs7761027	0.89[EUR][1000 genomes]
rs7769014	0.94[EUR][1000 genomes]
rs7775134	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56305600-56318600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:56305600-56319600	Weak transcription	HMEC	breast
3	chr6:56306600-56319000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:56309000-56321000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:56309400-56322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:56310400-56321000	Weak transcription	Left Ventricle	heart
8	chr6:56311600-56321000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:56313200-56322000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:56313200-56323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:56313400-56319000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:56313800-56322200	Weak transcription	NHLF	lung
13	chr6:56314000-56319400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:56314000-56319400	Enhancers	Liver	Liver
15	chr6:56314200-56321600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:56314400-56320800	Weak transcription	Brain Anterior Caudate	brain
17	chr6:56314400-56323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:56314600-56317200	Enhancers	Fetal Heart	heart
19	chr6:56314600-56317200	Enhancers	HepG2	liver
20	chr6:56315000-56322200	Weak transcription	GM12878-XiMat	blood
21	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr6:56315000-56349800	Strong transcription	HSMM	muscle
23	chr6:56315600-56317200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:56315600-56321000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:56315600-56322200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:56315800-56317200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:56315800-56319200	Weak transcription	NHDF-Ad	bronchial
29	chr6:56315800-56321800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:56315800-56322000	Weak transcription	Fetal Brain Male	brain
31	chr6:56315800-56323400	Weak transcription	Aorta	Aorta
32	chr6:56315800-56329200	Weak transcription	Small Intestine	intestine
33	chr6:56316000-56317800	Weak transcription	HSMMtube	muscle
34	chr6:56316000-56319200	Weak transcription	NH-A	brain
35	chr6:56316000-56323400	Weak transcription	Gastric	stomach
36	chr6:56316000-56323800	Weak transcription	Right Ventricle	heart
37	chr6:56316400-56317200	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr6:56316400-56319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:56316400-56320800	Weak transcription	Adipose Nuclei	Adipose
40	chr6:56316400-56322200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:56316400-56322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:56316400-56323800	Weak transcription	Fetal Intestine Small	intestine
43	chr6:56316600-56318000	Weak transcription	Fetal Intestine Large	intestine
44	chr6:56316600-56318400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:56316600-56319000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:56316600-56319400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:56316600-56320800	Weak transcription	Brain Substantia Nigra	brain
48	chr6:56316600-56321000	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:56316600-56321000	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:56316600-56322000	Weak transcription	Brain Cingulate Gyrus	brain

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