Variant report

Variant	rs12005463
Chromosome Location	chr9:93571448-93571449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93569248..93572925-chr9:93585588..93587867,3	K562	blood:
2	chr9:93561656..93565893-chr9:93566155..93575937,12	MCF-7	breast:
3	chr9:93566479..93568925-chr9:93571004..93572513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11792561	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550873	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552742	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12682953	1.00[ASN][1000 genomes]
rs12685847	1.00[ASN][1000 genomes]
rs12686576	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331504	1.00[ASN][1000 genomes]
rs1460836	1.00[ASN][1000 genomes]
rs17454793	1.00[ASN][1000 genomes]
rs62558478	1.00[ASN][1000 genomes]
rs62558479	1.00[ASN][1000 genomes]
rs62558496	1.00[ASN][1000 genomes]
rs62558501	1.00[ASN][1000 genomes]
rs62558503	1.00[ASN][1000 genomes]
rs62558550	1.00[ASN][1000 genomes]
rs62558551	1.00[ASN][1000 genomes]
rs62558552	1.00[ASN][1000 genomes]
rs62558553	1.00[ASN][1000 genomes]
rs62558555	1.00[ASN][1000 genomes]
rs62558557	1.00[ASN][1000 genomes]
rs62559062	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559063	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv893569	chr9:93552550-93587089	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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
7	esv1813758	chr9:93557698-93573095	Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12005463	SYK	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93564600-93572000	Weak transcription	Lung	lung
2	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:93565400-93577000	Weak transcription	Colonic Mucosa	Colon
4	chr9:93567000-93572800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:93567600-93573000	Weak transcription	NHEK	skin
6	chr9:93567800-93572000	Weak transcription	Esophagus	oesophagus
7	chr9:93567800-93572000	Weak transcription	K562	blood
8	chr9:93567800-93572400	Weak transcription	Stomach Mucosa	stomach
9	chr9:93567800-93584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:93567800-93584800	Weak transcription	Fetal Intestine Large	intestine
11	chr9:93567800-93597400	Weak transcription	Gastric	stomach
12	chr9:93568400-93575000	Enhancers	Fetal Thymus	thymus
13	chr9:93568400-93576600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:93568600-93573600	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr9:93569400-93573200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:93569600-93574600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:93569800-93571800	Enhancers	Fetal Kidney	kidney
18	chr9:93570000-93571600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:93570200-93571600	Genic enhancers	Duodenum Mucosa	Duodenum
20	chr9:93570200-93571600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr9:93570400-93571600	Enhancers	Primary hematopoietic stem cells	blood
22	chr9:93570400-93571800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
23	chr9:93570600-93572000	Flanking Active TSS	GM12878-XiMat	blood
24	chr9:93570800-93571600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr9:93571000-93573000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:93571000-93575200	Strong transcription	Fetal Intestine Small	intestine
27	chr9:93571200-93571800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:93571200-93572000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:93571200-93572400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr9:93571200-93572400	Weak transcription	Spleen	Spleen
31	chr9:93571200-93572800	Genic enhancers	Thymus	Thymus
32	chr9:93571200-93574000	Weak transcription	Pancreas	Pancrea
33	chr9:93571200-93576200	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr9:93571200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:93571400-93572200	Weak transcription	Fetal Stomach	stomach
36	chr9:93571400-93572600	Weak transcription	HMEC	breast
37	chr9:93571400-93572800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr9:93571400-93576600	Weak transcription	Small Intestine	intestine
39	chr9:93571400-93576800	Weak transcription	Primary T cells from cord blood	blood

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