Variant report

Variant	rs3789899
Chromosome Location	chr9:93615210-93615211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93598552..93601141-chr9:93613328..93615563,2	MCF-7	breast:
2	chr9:93562366..93565810-chr9:93615193..93619315,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10821511	0.90[ASN][1000 genomes]
rs10821514	0.91[ASN][1000 genomes]
rs10993707	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10993711	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12380445	0.88[ASN][1000 genomes]
rs17489429	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1864202	1.00[JPT][hapmap]
rs1993704	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2259147	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2387337	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2387339	0.90[ASN][1000 genomes]
rs3789898	0.90[ASN][1000 genomes]
rs4744016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744017	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7863711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv430078	chr9:93609668-93642766	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93599200-93616600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:93604400-93616200	Weak transcription	HMEC	breast
4	chr9:93604800-93616600	Weak transcription	NHEK	skin
5	chr9:93604800-93617200	Strong transcription	Spleen	Spleen
6	chr9:93605000-93616400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:93605000-93622800	Weak transcription	Adipose Nuclei	Adipose
8	chr9:93605000-93633000	Weak transcription	Fetal Kidney	kidney
9	chr9:93605200-93616400	Weak transcription	K562	blood
10	chr9:93605600-93615600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr9:93605600-93617400	Strong transcription	Thymus	Thymus
12	chr9:93605800-93621400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:93605800-93621600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:93605800-93631000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:93606000-93615600	Strong transcription	Fetal Thymus	thymus
16	chr9:93606000-93616600	Strong transcription	Fetal Intestine Small	intestine
17	chr9:93606000-93619600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:93606200-93615600	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr9:93606200-93615600	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:93606200-93616200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr9:93606200-93616400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:93606200-93616800	Strong transcription	Primary hematopoietic stem cells	blood
23	chr9:93606400-93616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:93606400-93616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:93606600-93615600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:93606600-93617400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:93606600-93619200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:93607000-93620000	Strong transcription	Primary B cells from cord blood	blood
29	chr9:93608200-93624400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:93610400-93624600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:93611200-93642200	Weak transcription	Stomach Mucosa	stomach
32	chr9:93611800-93620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:93612000-93616400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:93612400-93616400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:93612400-93623200	Weak transcription	Colonic Mucosa	Colon
36	chr9:93613200-93621800	Weak transcription	Pancreas	Pancrea
37	chr9:93613800-93616400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:93614600-93615400	Genic enhancers	Gastric	stomach
39	chr9:93614800-93623800	Weak transcription	Left Ventricle	heart
40	chr9:93615000-93615600	ZNF genes & repeats	Esophagus	oesophagus
41	chr9:93615000-93615600	ZNF genes & repeats	Lung	lung
42	chr9:93615000-93615600	Strong transcription	GM12878-XiMat	blood
43	chr9:93615000-93616800	Weak transcription	Fetal Lung	lung
44	chr9:93615200-93615600	Strong transcription	Fetal Intestine Large	intestine
45	chr9:93615200-93616800	Strong transcription	Fetal Stomach	stomach

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