Variant report

Variant	rs1152619
Chromosome Location	chr11:65255589-65255590
allele	A/C
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	chr11:65254355..65256226-chr11:65338919..65341693,2	MCF-7	breast:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
4	chr11:65255087..65257855-chr11:65337758..65339872,2	MCF-7	breast:
5	chr11:65255071..65255750-chr11:65264528..65265262,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245532	Chromatin interaction
ENSG00000120656	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000229388	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10896015	0.88[TSI][hapmap]
rs11227199	0.86[CEU][hapmap]
rs1152620	0.81[CEU][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1194076	0.88[TSI][hapmap]
rs1194338	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12270054	0.88[TSI][hapmap]
rs12360896	0.86[CEU][hapmap]
rs1621277	0.86[JPT][hapmap]
rs1626021	0.86[JPT][hapmap]
rs17146964	0.86[CEU][hapmap]
rs1784859	0.86[JPT][hapmap]
rs1787663	0.88[TSI][hapmap]
rs2846861	0.86[JPT][hapmap]
rs587080	0.80[AFR][1000 genomes]
rs588298	0.86[JPT][hapmap]
rs682845	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1152619	CDK2AP2	cis	cerebellum	SCAN
rs1152619	TPCN2	cis	parietal	SCAN
rs1152619	BBS1	cis	parietal	SCAN
rs1152619	TTC9C	cis	parietal	SCAN
rs1152619	INCENP	cis	cerebellum	SCAN
rs1152619	LTBP3	cis	cerebellum	SCAN
rs1152619	NEAT1	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65245600-65255600	Weak transcription	Gastric	stomach
2	chr11:65252200-65258200	Flanking Active TSS	Hela-S3	cervix
3	chr11:65252200-65259200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:65252400-65262400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:65252800-65262200	Enhancers	Liver	Liver
6	chr11:65252800-65262400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr11:65252800-65264400	Enhancers	Placenta	Placenta
8	chr11:65252800-65265200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr11:65253200-65255600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:65253200-65256200	Enhancers	K562	blood
11	chr11:65253200-65263800	Enhancers	Fetal Thymus	thymus
12	chr11:65253200-65264000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:65253400-65256600	Enhancers	Aorta	Aorta
14	chr11:65253400-65257400	Enhancers	Right Ventricle	heart
15	chr11:65253400-65264400	Enhancers	Left Ventricle	heart
16	chr11:65254000-65257800	Enhancers	Esophagus	oesophagus
17	chr11:65254000-65261200	Enhancers	Lung	lung
18	chr11:65254000-65261800	Enhancers	Psoas Muscle	Psoas
19	chr11:65254000-65263800	Enhancers	Right Atrium	heart
20	chr11:65254200-65256200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:65254200-65258200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:65254200-65258200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr11:65254200-65258400	Enhancers	Ovary	ovary
24	chr11:65254200-65262200	Enhancers	Fetal Intestine Large	intestine
25	chr11:65254200-65264200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr11:65254400-65257000	Enhancers	Primary hematopoietic stem cells	blood
27	chr11:65254400-65262200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:65254800-65255800	Flanking Active TSS	GM12878-XiMat	blood
29	chr11:65254800-65256600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr11:65254800-65259800	Enhancers	Primary B cells from cord blood	blood
31	chr11:65254800-65262200	Enhancers	Spleen	Spleen
32	chr11:65254800-65264200	Enhancers	Primary B cells from peripheral blood	blood
33	chr11:65255000-65255800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr11:65255000-65256000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:65255000-65256000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:65255000-65256200	Enhancers	Primary T cells from cord blood	blood
37	chr11:65255000-65256800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr11:65255000-65258200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr11:65255000-65262200	Enhancers	HUVEC	blood vessel
40	chr11:65255200-65255800	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr11:65255200-65255800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr11:65255200-65256000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr11:65255200-65256000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr11:65255200-65256000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr11:65255200-65256000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:65255200-65256000	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr11:65255200-65256400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr11:65255200-65256400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:65255200-65256400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr11:65255200-65256600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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