Variant report

Variant	rs1716836
Chromosome Location	chr3:120152861-120152862
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	chr3:120144896..120146989-chr3:120150144..120153389,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1147708	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1259330	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1259333	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259335	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1624195	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1628541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1733297	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1733302	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:120138200-120154200	Weak transcription	HMEC	breast
4	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:120138200-120169200	Weak transcription	Gastric	stomach
8	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
9	chr3:120140800-120154200	Weak transcription	Psoas Muscle	Psoas
10	chr3:120142000-120153600	Genic enhancers	NHLF	lung
11	chr3:120142400-120153600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:120143600-120154200	Genic enhancers	NH-A	brain
13	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:120145400-120157600	Weak transcription	Fetal Brain Female	brain
15	chr3:120145600-120153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
17	chr3:120146800-120157800	Weak transcription	Fetal Brain Male	brain
18	chr3:120147000-120154400	Genic enhancers	HSMMtube	muscle
19	chr3:120147200-120154400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:120147600-120153200	Genic enhancers	HSMM	muscle
21	chr3:120147600-120154000	Genic enhancers	Muscle Satellite Cultured Cells	--
22	chr3:120147600-120154200	Weak transcription	Fetal Intestine Small	intestine
23	chr3:120148000-120153600	Enhancers	Fetal Heart	heart
24	chr3:120148000-120161000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:120149000-120161200	Genic enhancers	NHDF-Ad	bronchial
26	chr3:120149200-120154200	Weak transcription	Small Intestine	intestine
27	chr3:120149200-120155400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:120149200-120156600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:120149400-120155600	Enhancers	Colon Smooth Muscle	Colon
30	chr3:120149400-120157200	Weak transcription	Colonic Mucosa	Colon
31	chr3:120149800-120154000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:120150000-120153200	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:120150400-120154200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:120150400-120157400	Weak transcription	Fetal Intestine Large	intestine
35	chr3:120150600-120153000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:120150600-120153600	Enhancers	Right Atrium	heart
37	chr3:120150800-120153000	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr3:120151200-120155400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:120151400-120154200	Weak transcription	Brain Angular Gyrus	brain
40	chr3:120151400-120154200	Weak transcription	Stomach Mucosa	stomach
41	chr3:120151600-120153000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:120151600-120153400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:120151800-120153400	Genic enhancers	Left Ventricle	heart
44	chr3:120151800-120154000	Weak transcription	A549	lung
45	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:120152000-120153200	Enhancers	Spleen	Spleen
47	chr3:120152000-120153800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:120152000-120154200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:120152000-120154200	Genic enhancers	Osteobl	bone
50	chr3:120152000-120155200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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