Variant report

Variant	rs16860787
Chromosome Location	chr3:113003924-113003925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113000767..113002903-chr3:113003436..113005899,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10511323	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11710894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919134	0.81[JPT][hapmap];0.94[AMR][1000 genomes]
rs11928342	0.86[AMR][1000 genomes]
rs12485329	0.93[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12492273	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12494864	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12631733	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638030	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16860758	0.91[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16860792	0.85[AMR][1000 genomes]
rs2036282	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2270781	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs34284771	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814398	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846046	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856719	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271357	0.90[AMR][1000 genomes]
rs4682131	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682132	0.93[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682478	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682479	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682483	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682485	0.83[JPT][hapmap]
rs6809516	0.80[JPT][hapmap]
rs73235143	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73235147	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7641410	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs775222	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820386	0.83[JPT][hapmap]
rs9857414	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112990600-113004000	Weak transcription	NHEK	skin
4	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
6	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
11	chr3:112995400-113035800	Weak transcription	Lung	lung
12	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:112995800-113004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:112995800-113006600	Weak transcription	Fetal Brain Male	brain
16	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
18	chr3:112996000-113005800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
20	chr3:112996200-113004400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:112996200-113005800	Weak transcription	Osteobl	bone
22	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:112996400-113004600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:112996600-113004200	Strong transcription	Colon Smooth Muscle	Colon
26	chr3:112996800-113004200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:112997000-113004000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:112997000-113004000	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:112997000-113005200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:112997000-113006200	Strong transcription	Fetal Intestine Small	intestine
31	chr3:112997200-113005400	Strong transcription	Rectal Smooth Muscle	rectum
32	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
33	chr3:112997400-113004000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:112997400-113004400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:112997400-113006200	Strong transcription	Fetal Stomach	stomach
36	chr3:112997600-113004600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:112997800-113005200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:112998200-113005000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:112998400-113004000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:112998600-113036000	Weak transcription	Gastric	stomach
41	chr3:112999600-113004200	Strong transcription	Brain Substantia Nigra	brain
42	chr3:113000200-113006000	Weak transcription	HSMMtube	muscle
43	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:113000400-113004200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:113000800-113005200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:113000800-113014400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:113001000-113006000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:113001200-113006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
50	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney

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