Variant report

Variant	rs3753003
Chromosome Location	chr9:7174433-7174434
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:7163757..7166355-chr9:7173278..7174995,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1041288	0.89[ASN][1000 genomes]
rs10758842	0.98[ASN][1000 genomes]
rs10815534	0.98[ASN][1000 genomes]
rs10976118	0.88[ASN][1000 genomes]
rs10976119	0.89[ASN][1000 genomes]
rs1467700	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1887870	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1887871	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1928211	0.96[ASN][1000 genomes]
rs2011128	0.90[ASN][1000 genomes]
rs2014332	0.91[ASN][1000 genomes]
rs2026709	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026714	0.81[EUR][1000 genomes]
rs2094613	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2104682	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2248904	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2381570	0.81[AMR][1000 genomes]
rs2381571	0.95[ASN][1000 genomes]
rs2381572	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2494241	0.89[ASN][1000 genomes]
rs2770731	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2770732	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2770734	0.84[AMR][1000 genomes]
rs2770735	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2770736	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2770737	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2770741	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2770756	0.88[ASN][1000 genomes]
rs2770760	0.88[ASN][1000 genomes]
rs2820910	0.89[ASN][1000 genomes]
rs2820920	0.81[AMR][1000 genomes]
rs2820922	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2820923	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2820924	0.97[ASN][1000 genomes]
rs2820926	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2820927	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2820928	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2820929	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2820931	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3753002	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3829103	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7022054	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7022345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7029684	1.00[ASN][1000 genomes]
rs7036627	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7874501	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs913584	0.81[AMR][1000 genomes]
rs913587	0.88[AMR][1000 genomes]
rs913589	0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs913590	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs913591	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943925	0.99[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	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892192	chr9:7153009-7257340	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv528873	chr9:7163530-7177936	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7147400-7174600	Weak transcription	NHEK	skin
2	chr9:7148600-7185400	Weak transcription	HMEC	breast
3	chr9:7149600-7185400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:7149600-7186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:7150400-7175800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:7151800-7188600	Weak transcription	Colonic Mucosa	Colon
7	chr9:7160800-7175200	Strong transcription	Primary B cells from cord blood	blood
8	chr9:7160800-7182000	Weak transcription	Dnd41	blood
9	chr9:7162600-7181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:7162600-7182200	Weak transcription	Small Intestine	intestine
11	chr9:7163200-7177800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr9:7163400-7180600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:7163800-7179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:7164000-7174600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:7164000-7176200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:7164600-7178000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr9:7165800-7174600	Weak transcription	Ovary	ovary
18	chr9:7165800-7176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:7165800-7179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:7165800-7183800	Weak transcription	Esophagus	oesophagus
21	chr9:7165800-7185400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:7166000-7175600	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:7166200-7181000	Weak transcription	Hela-S3	cervix
24	chr9:7166400-7174600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:7166400-7176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:7167200-7185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:7168000-7174600	Weak transcription	Pancreas	Pancrea
28	chr9:7168200-7176400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:7169200-7183000	Strong transcription	Primary T cells from cord blood	blood
30	chr9:7169400-7176600	Strong transcription	Fetal Intestine Large	intestine
31	chr9:7169600-7175000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:7169600-7176400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:7169600-7176600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:7169600-7176800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:7169800-7176600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:7169800-7176600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr9:7169800-7176800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr9:7169800-7177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:7170000-7176400	Strong transcription	Adipose Nuclei	Adipose
40	chr9:7170000-7176400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr9:7170800-7176600	Enhancers	Placenta	Placenta
42	chr9:7171000-7175000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:7171000-7175000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr9:7171000-7176400	Strong transcription	Thymus	Thymus
45	chr9:7171200-7188200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:7171200-7193000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:7172000-7174600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:7172000-7182400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:7172000-7183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:7172200-7175000	Enhancers	Skeletal Muscle Female	skeletal muscle

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