Variant report

Variant	rs17489214
Chromosome Location	chr9:93603138-93603139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11787537	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12004706	0.86[ASN][1000 genomes]
rs12555502	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35758162	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222210	0.86[ASN][1000 genomes]
rs62559143	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559145	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559146	1.00[ASN][1000 genomes]
rs7030222	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729051	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	esv3392644	chr9:93602031-93605929	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3433405	chr9:93602131-93606129	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3411483	chr9:93602131-93606229	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17489214	ZNF484	cis	cerebellum	SCAN
rs17489214	ZNF484	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:93580800-93603400	Weak transcription	K562	blood
4	chr9:93585600-93607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:93589200-93606000	Weak transcription	Colonic Mucosa	Colon
6	chr9:93591000-93603200	Weak transcription	Fetal Kidney	kidney
7	chr9:93593600-93603400	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr9:93595800-93603200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:93595800-93603200	Weak transcription	NHEK	skin
10	chr9:93595800-93606600	Weak transcription	Stomach Mucosa	stomach
11	chr9:93596000-93607600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:93598000-93603200	Weak transcription	Pancreas	Pancrea
13	chr9:93598200-93606600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:93599200-93616600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:93599800-93603400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:93600200-93606400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:93600200-93613800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:93601000-93603400	Weak transcription	Fetal Lung	lung
19	chr9:93601000-93603400	Weak transcription	Gastric	stomach
20	chr9:93601600-93604800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:93601800-93603200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:93602000-93606600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:93602200-93603600	Enhancers	GM12878-XiMat	blood
25	chr9:93602200-93604200	Weak transcription	Thymus	Thymus
26	chr9:93602200-93605400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:93602400-93603400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:93602400-93604200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:93602400-93606000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:93602600-93603200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr9:93602600-93603200	Weak transcription	Esophagus	oesophagus
32	chr9:93602600-93603200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr9:93602600-93603400	Enhancers	Fetal Muscle Leg	muscle
34	chr9:93602600-93603600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:93602600-93604400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:93602600-93604600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:93602600-93606000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:93602600-93606000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:93602600-93606000	Weak transcription	Fetal Intestine Small	intestine
40	chr9:93602600-93609200	Weak transcription	Right Ventricle	heart
41	chr9:93602800-93604400	Weak transcription	Fetal Thymus	thymus
42	chr9:93602800-93604800	Strong transcription	Primary B cells from cord blood	blood
43	chr9:93602800-93605400	Weak transcription	Fetal Stomach	stomach
44	chr9:93603000-93603200	Genic enhancers	Spleen	Spleen

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