Variant report

Variant	rs1733299
Chromosome Location	chr3:120152050-120152051
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	chr3:120144896..120146989-chr3:120150144..120153389,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1123897	0.97[ASN][1000 genomes]
rs1123898	0.95[ASN][1000 genomes]
rs1147706	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1147709	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1147710	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259311	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1259329	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1259331	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259332	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259334	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1259336	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1259337	1.00[CEU][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1259338	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1259339	0.85[ASN][1000 genomes]
rs1259471	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259472	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259473	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1267675	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1270209	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520881	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1716837	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733298	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733301	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733303	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733304	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733306	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733307	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733319	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2700263	0.85[ASN][1000 genomes]
rs2702155	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5000757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6768839	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs874477	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs874478	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs874479	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs874480	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9631455	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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:91 , 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	chr3:120144400-120152600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:120145400-120157600	Weak transcription	Fetal Brain Female	brain
16	chr3:120145600-120153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
18	chr3:120146400-120152400	Weak transcription	NHEK	skin
19	chr3:120146800-120157800	Weak transcription	Fetal Brain Male	brain
20	chr3:120147000-120154400	Genic enhancers	HSMMtube	muscle
21	chr3:120147200-120154400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:120147600-120153200	Genic enhancers	HSMM	muscle
23	chr3:120147600-120154000	Genic enhancers	Muscle Satellite Cultured Cells	--
24	chr3:120147600-120154200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:120148000-120153600	Enhancers	Fetal Heart	heart
26	chr3:120148000-120161000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:120149000-120152600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:120149000-120161200	Genic enhancers	NHDF-Ad	bronchial
29	chr3:120149200-120152600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:120149200-120154200	Weak transcription	Small Intestine	intestine
31	chr3:120149200-120155400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:120149200-120156600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:120149400-120155600	Enhancers	Colon Smooth Muscle	Colon
34	chr3:120149400-120157200	Weak transcription	Colonic Mucosa	Colon
35	chr3:120149800-120154000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:120150000-120152800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:120150000-120153200	Enhancers	Rectal Smooth Muscle	rectum
38	chr3:120150400-120152800	Enhancers	Fetal Lung	lung
39	chr3:120150400-120154200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:120150400-120157400	Weak transcription	Fetal Intestine Large	intestine
41	chr3:120150600-120152200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr3:120150600-120152200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:120150600-120152200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:120150600-120152200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:120150600-120152200	Enhancers	Right Ventricle	heart
46	chr3:120150600-120152400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:120150600-120152400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr3:120150600-120152600	Enhancers	Aorta	Aorta
49	chr3:120150600-120152600	Enhancers	Fetal Kidney	kidney
50	chr3:120150600-120152600	Enhancers	Fetal Muscle Leg	muscle

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