Variant report

Variant	rs3739460
Chromosome Location	chr9:2814615-2814616
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:2813339..2814920-chr9:2817928..2820182,2	MCF-7	breast:
2	chr9:2812122..2814985-chr9:2820250..2822409,2	K562	blood:
3	chr9:2808764..2811961-chr9:2812459..2815898,4	K562	blood:
4	chr9:2814055..2816389-chr9:2820245..2822850,2	MCF-7	breast:
5	chr9:2813165..2815456-chr9:2815633..2818470,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10116824	0.81[CEU][hapmap]
rs10125846	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs10217194	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10481516	0.85[CEU][hapmap]
rs10733433	0.84[EUR][1000 genomes]
rs10738791	0.82[CEU][hapmap]
rs10738792	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10757713	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10757715	0.81[CEU][hapmap]
rs10812719	0.81[CEU][hapmap]
rs10812760	0.89[EUR][1000 genomes]
rs10968361	0.81[CEU][hapmap]
rs1875440	0.84[EUR][1000 genomes]
rs1875441	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2173904	0.89[CEU][hapmap]
rs2270888	0.84[CHB][hapmap]
rs2292000	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3824350	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs3824351	0.85[CEU][hapmap]
rs4439183	0.85[CEU][hapmap]
rs6476038	0.93[CEU][hapmap]
rs6476047	0.81[CEU][hapmap]
rs7036752	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7850317	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv892082	chr9:2699606-2833267	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2791600-2815800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:2791800-2821800	Strong transcription	Primary T cells from cord blood	blood
3	chr9:2792000-2822200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:2793200-2826600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:2794400-2814800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:2795200-2817600	Weak transcription	Stomach Mucosa	stomach
7	chr9:2796400-2822200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:2798000-2837400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:2801200-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:2801600-2837200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:2803600-2829200	Weak transcription	Small Intestine	intestine
12	chr9:2805800-2829400	Weak transcription	Fetal Brain Male	brain
13	chr9:2808800-2827000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:2809200-2818000	Weak transcription	Right Atrium	heart
15	chr9:2810400-2816400	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:2810400-2827400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:2810600-2824000	Weak transcription	Fetal Kidney	kidney
18	chr9:2810800-2816200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:2811400-2815800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:2811600-2815400	Weak transcription	Fetal Stomach	stomach
21	chr9:2811600-2815400	Weak transcription	Ovary	ovary
22	chr9:2811600-2815800	Weak transcription	Aorta	Aorta
23	chr9:2811600-2816000	Weak transcription	HSMMtube	muscle
24	chr9:2811600-2816200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:2811600-2816400	Weak transcription	Pancreas	Pancrea
26	chr9:2811600-2816600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:2811600-2818600	Weak transcription	Fetal Brain Female	brain
28	chr9:2811600-2824000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:2811600-2824200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:2811600-2824200	Weak transcription	Brain Anterior Caudate	brain
31	chr9:2811600-2824200	Weak transcription	Psoas Muscle	Psoas
32	chr9:2811600-2824600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:2811600-2824600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:2811600-2824600	Weak transcription	Esophagus	oesophagus
35	chr9:2811600-2826200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:2811600-2826200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:2811600-2826200	Weak transcription	Brain Germinal Matrix	brain
38	chr9:2811600-2827600	Weak transcription	Gastric	stomach
39	chr9:2811600-2827600	Weak transcription	Right Ventricle	heart
40	chr9:2811600-2827600	Weak transcription	Thymus	Thymus
41	chr9:2811600-2827600	Weak transcription	Spleen	Spleen
42	chr9:2811600-2827800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:2811600-2827800	Weak transcription	Fetal Intestine Small	intestine
44	chr9:2811600-2828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:2811600-2828200	Weak transcription	Colonic Mucosa	Colon
46	chr9:2811600-2842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:2811800-2815600	Weak transcription	NHLF	lung
48	chr9:2811800-2815800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:2811800-2816400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:2811800-2818000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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