Variant report

Variant	rs9853439
Chromosome Location	chr3:112997743-112997744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112995543..112998104-chr3:113010327..113013877,3	MCF-7	breast:
2	chr3:112986625..112989851-chr3:112997054..112999009,3	MCF-7	breast:
3	chr3:112769775..112770734-chr3:112996923..112997769,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction
ENSG00000206530	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511324	0.90[EUR][1000 genomes]
rs13326562	0.81[EUR][1000 genomes]
rs1499898	0.91[AFR][1000 genomes]
rs16860720	0.91[AFR][1000 genomes]
rs16860734	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28679287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3995908	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6438134	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap]
rs6780720	1.00[CEU][hapmap]
rs6808103	1.00[CEU][hapmap]
rs7625829	1.00[CEU][hapmap]
rs7629636	1.00[CEU][hapmap]
rs7652801	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9288980	0.90[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap]
rs9811168	0.81[EUR][1000 genomes]
rs9819129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820139	0.91[AFR][1000 genomes]
rs9820627	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823770	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831049	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832953	0.83[YRI][hapmap];0.95[AFR][1000 genomes]
rs9836199	0.81[EUR][1000 genomes]
rs9837357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840485	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851183	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9852068	1.00[CEU][hapmap]
rs9863114	0.81[EUR][1000 genomes]
rs9864630	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872998	0.83[AFR][1000 genomes]

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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112990600-113004000	Weak transcription	NHEK	skin
6	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
8	chr3:112994200-112997800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:112995200-112999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:112995200-113001200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:112995400-112998200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
17	chr3:112995400-113035800	Weak transcription	Lung	lung
18	chr3:112995600-112998200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112995800-112998400	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:112995800-112998400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr3:112995800-112999400	Weak transcription	Fetal Kidney	kidney
24	chr3:112995800-112999600	Weak transcription	HSMMtube	muscle
25	chr3:112995800-113004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:112995800-113006600	Weak transcription	Fetal Brain Male	brain
27	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
29	chr3:112996000-112997800	Weak transcription	Brain Germinal Matrix	brain
30	chr3:112996000-112998000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:112996000-113000000	Weak transcription	Pancreas	Pancrea
32	chr3:112996000-113005800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
34	chr3:112996200-112997800	Enhancers	Brain Hippocampus Middle	brain
35	chr3:112996200-112997800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:112996200-112998400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:112996200-112999400	Weak transcription	Fetal Thymus	thymus
38	chr3:112996200-113000400	Weak transcription	Stomach Mucosa	stomach
39	chr3:112996200-113000400	Strong transcription	NHDF-Ad	bronchial
40	chr3:112996200-113001200	Strong transcription	Fetal Lung	lung
41	chr3:112996200-113002000	Weak transcription	NH-A	brain
42	chr3:112996200-113003000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:112996200-113004400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:112996200-113005800	Weak transcription	Osteobl	bone
45	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:112996400-113003600	Weak transcription	Brain Angular Gyrus	brain
47	chr3:112996400-113004600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:112996600-112997800	Enhancers	GM12878-XiMat	blood
50	chr3:112996600-112998800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland

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