Variant report

Variant	rs3789902
Chromosome Location	chr9:93620384-93620385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93563040..93565332-chr9:93619381..93621543,3	MCF-7	breast:
2	chr9:93612250..93614199-chr9:93619484..93621935,2	MCF-7	breast:
3	chr9:93571707..93573621-chr9:93620166..93622474,2	MCF-7	breast:
4	chr9:93619506..93622175-chr9:93629106..93631175,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10124093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993722	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10993723	0.82[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993724	0.82[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993725	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10993728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10993729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12000793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12006330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2306040	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35478826	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36063880	0.97[ASN][1000 genomes]
rs3789903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789909	0.82[EUR][1000 genomes]
rs4529574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4744019	0.82[CHB][hapmap]
rs4744516	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4744517	0.82[AMR][1000 genomes]
rs7866696	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:93605000-93622800	Weak transcription	Adipose Nuclei	Adipose
3	chr9:93605000-93633000	Weak transcription	Fetal Kidney	kidney
4	chr9:93605800-93621400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:93605800-93621600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr9:93605800-93631000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:93608200-93624400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:93610400-93624600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:93611200-93642200	Weak transcription	Stomach Mucosa	stomach
10	chr9:93611800-93620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:93612400-93623200	Weak transcription	Colonic Mucosa	Colon
12	chr9:93613200-93621800	Weak transcription	Pancreas	Pancrea
13	chr9:93614800-93623800	Weak transcription	Left Ventricle	heart
14	chr9:93615400-93624000	Weak transcription	Gastric	stomach
15	chr9:93615600-93623200	Weak transcription	Esophagus	oesophagus
16	chr9:93615600-93623600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:93616800-93624400	Weak transcription	Lung	lung
18	chr9:93617200-93624000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:93617200-93640600	Weak transcription	K562	blood
20	chr9:93617400-93622600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:93617400-93622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:93617400-93629600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:93617400-93640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:93617600-93623400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:93617800-93640600	Weak transcription	NHEK	skin
26	chr9:93619000-93620600	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr9:93619000-93623800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr9:93619200-93621200	Genic enhancers	Fetal Thymus	thymus
29	chr9:93619200-93621400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr9:93619200-93623600	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr9:93619400-93621600	Enhancers	Primary T cells from cord blood	blood
32	chr9:93619400-93630000	Strong transcription	Thymus	Thymus
33	chr9:93619600-93621600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:93619800-93620400	Strong transcription	Spleen	Spleen
35	chr9:93619800-93620600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:93619800-93620600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:93619800-93621000	Strong transcription	Fetal Stomach	stomach
38	chr9:93619800-93622200	Strong transcription	Fetal Intestine Large	intestine
39	chr9:93619800-93622800	Weak transcription	GM12878-XiMat	blood
40	chr9:93619800-93627000	Strong transcription	Fetal Intestine Small	intestine
41	chr9:93620000-93621200	Genic enhancers	Primary B cells from cord blood	blood
42	chr9:93620200-93620600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:93620200-93623000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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