Variant report

Variant	rs2562396
Chromosome Location	chr9:93567425-93567426
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93566139..93567654-chr9:93575721..93577420,2	MCF-7	breast:
2	chr9:93561656..93565893-chr9:93566155..93575937,12	MCF-7	breast:
3	chr9:93566479..93568925-chr9:93571004..93572513,2	MCF-7	breast:
4	chr9:93566130..93568297-chr9:93575356..93577751,2	K562	blood:
5	chr9:93566333..93568000-chr9:93577767..93579301,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10448310	0.80[ASN][1000 genomes]
rs10993693	0.90[CHB][hapmap]
rs12350798	0.91[CHB][hapmap]
rs1319677	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333630	0.87[CHB][hapmap]
rs1333632	0.89[ASN][1000 genomes]
rs1333633	0.81[ASN][1000 genomes]
rs1333634	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333635	0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333637	0.80[ASN][1000 genomes]
rs188313	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562397	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2613308	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2774260	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780701	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780702	0.87[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290266	0.86[AMR][1000 genomes]
rs290268	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs290271	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs290274	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs290276	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs290987	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290988	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290989	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290990	0.96[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290991	0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290993	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290994	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290997	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291006	0.86[AMR][1000 genomes]
rs772407	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7856021	0.87[CHB][hapmap]
rs914925	0.87[CHB][hapmap]
rs94626	0.86[AMR][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	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
8	esv275555	chr9:93565999-93570451	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2562396	SYK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93563200-93568000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:93563800-93567600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr9:93564600-93567600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:93564600-93568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:93564600-93572000	Weak transcription	Lung	lung
6	chr9:93564800-93567800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:93565000-93569400	Weak transcription	Primary T cells from cord blood	blood
8	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:93565200-93567800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr9:93565200-93568400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr9:93565400-93567600	Enhancers	NHEK	skin
12	chr9:93565400-93570600	Weak transcription	HMEC	breast
13	chr9:93565400-93570800	Weak transcription	Placenta	Placenta
14	chr9:93565400-93577000	Weak transcription	Colonic Mucosa	Colon
15	chr9:93565600-93567800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr9:93566200-93567800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr9:93566200-93567800	Enhancers	Fetal Lung	lung
18	chr9:93566600-93567600	Enhancers	Fetal Intestine Small	intestine
19	chr9:93566800-93567600	Enhancers	Dnd41	blood
20	chr9:93566800-93567800	Enhancers	K562	blood
21	chr9:93566800-93568400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr9:93566800-93569200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:93567000-93567800	Enhancers	Fetal Intestine Large	intestine
24	chr9:93567000-93572800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:93567200-93568000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:93567200-93568600	Flanking Active TSS	GM12878-XiMat	blood
27	chr9:93567400-93567600	Flanking Active TSS	Fetal Kidney	kidney
28	chr9:93567400-93567600	Enhancers	Fetal Thymus	thymus
29	chr9:93567400-93567800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:93567400-93567800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr9:93567400-93567800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:93567400-93567800	Enhancers	Brain Germinal Matrix	brain
33	chr9:93567400-93567800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr9:93567400-93567800	Enhancers	Esophagus	oesophagus
35	chr9:93567400-93567800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr9:93567400-93567800	Enhancers	Gastric	stomach
37	chr9:93567400-93567800	Enhancers	Pancreas	Pancrea
38	chr9:93567400-93567800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr9:93567400-93567800	Enhancers	Small Intestine	intestine
40	chr9:93567400-93567800	Enhancers	Stomach Mucosa	stomach
41	chr9:93567400-93567800	Flanking Active TSS	Thymus	Thymus
42	chr9:93567400-93567800	Enhancers	Spleen	Spleen
43	chr9:93567400-93568000	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr9:93567400-93570000	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links