Variant report

Variant	rs588298
Chromosome Location	chr11:65253574-65253575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:28968709..28970596-chr11:65253553..65255713,2	K562	blood:
2	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
3	chr11:65251502..65254034-chr11:65343367..65344998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120656	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000229388	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10896001	0.81[AMR][1000 genomes]
rs11227204	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1152619	0.86[JPT][hapmap]
rs1616810	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1621277	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1626021	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784100	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784101	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784858	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784859	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105608	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508711	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2508712	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2846861	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957268	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2957269	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015965	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015966	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3016343	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132742	0.84[AMR][1000 genomes]
rs3132743	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3132767	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512715	0.83[MEX][hapmap]
rs587080	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs587390	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs591291	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs600231	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs602838	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604676	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605035	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs660588	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs661403	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs674485	0.83[MEX][hapmap]
rs682845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694243	0.83[MEX][hapmap]
rs7114809	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934628	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
18	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
19	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
20	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
21	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs588298	NEAT1	cis	Esophagus Muscularis	GTEx
rs588298	PYGM	cis	cerebellum	SCAN
rs588298	NEAT1	cis	Esophagus Mucosa	GTEx
rs588298	LTBP3	cis	cerebellum	SCAN
rs588298	NEAT1	cis	Muscle Skeletal	GTEx
rs588298	SCGB2A2	cis	parietal	SCAN
rs588298	NEAT1	cis	Nerve Tibial	GTEx
rs588298	INCENP	cis	cerebellum	SCAN
rs588298	BBS1	cis	parietal	SCAN
rs588298	VWCE	cis	parietal	SCAN
rs588298	CDK2AP2	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65245400-65254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:65245600-65255600	Weak transcription	Gastric	stomach
3	chr11:65246400-65254200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:65246400-65254800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:65247400-65254800	Weak transcription	Spleen	Spleen
6	chr11:65247600-65254000	Weak transcription	Psoas Muscle	Psoas
7	chr11:65247600-65254200	Weak transcription	Fetal Intestine Large	intestine
8	chr11:65247800-65254200	Weak transcription	Fetal Lung	lung
9	chr11:65247800-65254400	Weak transcription	Colonic Mucosa	Colon
10	chr11:65247800-65254400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:65249200-65254200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:65249400-65254000	Weak transcription	Right Atrium	heart
13	chr11:65249400-65254200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:65249400-65254400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:65249400-65254400	Enhancers	Brain Hippocampus Middle	brain
16	chr11:65250000-65254000	Weak transcription	HUVEC	blood vessel
17	chr11:65250200-65254200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr11:65250200-65254200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:65250400-65254000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:65250400-65254200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:65250400-65254200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:65251000-65254200	Weak transcription	Ovary	ovary
23	chr11:65251400-65254400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:65251400-65255400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:65252200-65253600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr11:65252200-65253600	Enhancers	Small Intestine	intestine
27	chr11:65252200-65254200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:65252200-65254200	Enhancers	Brain Cingulate Gyrus	brain
29	chr11:65252200-65254400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:65252200-65254600	Enhancers	Brain Anterior Caudate	brain
31	chr11:65252200-65254600	Enhancers	Fetal Brain Male	brain
32	chr11:65252200-65254600	Enhancers	NHDF-Ad	bronchial
33	chr11:65252200-65255200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr11:65252200-65255400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr11:65252200-65255400	Enhancers	NHLF	lung
36	chr11:65252200-65258200	Flanking Active TSS	Hela-S3	cervix
37	chr11:65252200-65259200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:65252400-65254200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:65252400-65255400	Enhancers	Rectal Smooth Muscle	rectum
40	chr11:65252400-65255400	Enhancers	Stomach Mucosa	stomach
41	chr11:65252400-65262400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:65252600-65253600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:65252600-65255200	Enhancers	Brain Substantia Nigra	brain
44	chr11:65252600-65255400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:65252600-65255400	Enhancers	Fetal Intestine Small	intestine
46	chr11:65252600-65255400	Enhancers	Fetal Muscle Trunk	muscle
47	chr11:65252600-65255400	Enhancers	Fetal Muscle Leg	muscle
48	chr11:65252800-65253600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:65252800-65253600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:65252800-65253600	Flanking Active TSS	HepG2	liver

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