Variant report

Variant	rs16860752
Chromosome Location	chr3:112986543-112986544
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112980495..112983266-chr3:112984401..112987231,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11917869	1.00[AMR][1000 genomes]
rs11919091	1.00[AMR][1000 genomes]
rs11920233	1.00[AMR][1000 genomes]
rs11922003	1.00[AMR][1000 genomes]
rs11925633	1.00[AMR][1000 genomes]
rs11926656	1.00[AMR][1000 genomes]
rs11929188	1.00[AMR][1000 genomes]
rs13316462	1.00[ASW][hapmap]
rs16845110	1.00[AMR][1000 genomes]
rs16860700	1.00[AMR][1000 genomes]
rs16860716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860732	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860748	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860782	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860800	1.00[AMR][1000 genomes]
rs16860854	1.00[AMR][1000 genomes]
rs16860875	1.00[AMR][1000 genomes]
rs16861019	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs2399476	0.83[AFR][1000 genomes]
rs4082653	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs7430385	1.00[AMR][1000 genomes]
rs7651839	1.00[AMR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
7	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:112976400-112988600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:112981000-112986600	Enhancers	Brain Substantia Nigra	brain
11	chr3:112981200-112991000	Genic enhancers	Fetal Muscle Leg	muscle
12	chr3:112981400-112987200	Weak transcription	Aorta	Aorta
13	chr3:112981400-112989800	Weak transcription	Gastric	stomach
14	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:112982000-112989800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:112982200-112987200	Weak transcription	Fetal Intestine Large	intestine
17	chr3:112982200-112988800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:112982200-112989400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:112982600-112989000	Weak transcription	NHEK	skin
20	chr3:112982800-112993600	Weak transcription	HMEC	breast
21	chr3:112983000-112987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:112983000-112987400	Weak transcription	NHDF-Ad	bronchial
23	chr3:112983400-112986800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:112983800-112995000	Weak transcription	Lung	lung
25	chr3:112984000-112986600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:112984000-112987000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
28	chr3:112984200-112987000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:112984200-112987200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:112984200-112987200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:112984200-112987400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:112984200-112987800	Weak transcription	Pancreas	Pancrea
33	chr3:112984200-112989800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:112984200-112994400	Weak transcription	HSMM	muscle
36	chr3:112984400-112987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:112984400-112987200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:112984600-112988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:112984600-112989800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:112984600-112991200	Weak transcription	Brain Germinal Matrix	brain
41	chr3:112984600-112993400	Weak transcription	Fetal Brain Male	brain
42	chr3:112984800-112986600	Strong transcription	Fetal Stomach	stomach
43	chr3:112984800-112987600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:112984800-112988600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:112984800-112992400	Weak transcription	Fetal Thymus	thymus
46	chr3:112984800-112993000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:112985000-112987600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:112985400-112986600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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