Variant report

Variant	rs7649661
Chromosome Location	chr3:119670140-119670141
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119643647..119646085-chr3:119668156..119670521,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11921053	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12494560	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13314595	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1579031	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16830689	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1719889	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2037547	0.82[AMR][1000 genomes]
rs2461827	0.82[AMR][1000 genomes]
rs28516957	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs334535	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs334536	0.86[EUR][1000 genomes]
rs334559	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs334560	0.86[EUR][1000 genomes]
rs334566	0.86[EUR][1000 genomes]
rs4072520	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4450859	0.93[AMR][1000 genomes]
rs56126162	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58043853	0.81[EUR][1000 genomes]
rs6438555	0.86[EUR][1000 genomes]
rs66650215	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6769435	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770314	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771023	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6774693	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6775397	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6779828	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6790751	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6795874	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6802301	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7613197	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7617372	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7620750	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7624540	0.82[AMR][1000 genomes]
rs7636600	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7652172	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9289138	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs968824	0.86[EUR][1000 genomes]
rs9851174	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9859778	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9879992	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][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	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	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
3	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
4	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
5	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:119640600-119672400	Weak transcription	Osteobl	bone
7	chr3:119641000-119681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:119641000-119681600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:119641000-119694400	Weak transcription	Fetal Lung	lung
10	chr3:119641200-119681200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:119656400-119680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:119656400-119681200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:119656400-119700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:119656600-119718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:119658400-119688400	Weak transcription	NHEK	skin
16	chr3:119658400-119688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:119662000-119684800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:119662400-119700400	Weak transcription	Fetal Intestine Large	intestine
19	chr3:119663600-119681200	Weak transcription	Primary T cells from cord blood	blood
20	chr3:119664000-119695000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:119664200-119674400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:119664600-119673600	Weak transcription	Small Intestine	intestine
23	chr3:119664600-119700200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:119664600-119702400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:119665800-119671000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:119665800-119697400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:119665800-119716800	Weak transcription	HSMM	muscle
28	chr3:119666000-119679800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:119666000-119703000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:119666200-119671200	Weak transcription	HUVEC	blood vessel
31	chr3:119666200-119673400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:119666200-119680600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:119666200-119680600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:119666200-119687600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:119666200-119688200	Weak transcription	HMEC	breast
36	chr3:119666200-119700200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:119666200-119700400	Weak transcription	Fetal Thymus	thymus
38	chr3:119666400-119673800	Weak transcription	NHDF-Ad	bronchial
39	chr3:119666400-119677800	Weak transcription	Primary B cells from cord blood	blood
40	chr3:119666400-119681200	Weak transcription	Dnd41	blood
41	chr3:119666400-119681200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:119666400-119681600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr3:119666400-119688400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:119667200-119688600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:119667800-119688000	Weak transcription	Pancreas	Pancrea
46	chr3:119669000-119670200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr3:119669200-119670200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:119669200-119670400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr3:119669200-119671000	Enhancers	Adipose Nuclei	Adipose
50	chr3:119669200-119672200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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