Variant report

Variant	rs11658564
Chromosome Location	chr17:16023587-16023588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16015557..16017498-chr17:16021823..16023792,2	MCF-7	breast:
2	chr13:21346241..21348378-chr17:16020761..16023781,3	MCF-7	breast:
3	chr17:16019669..16022129-chr17:16022606..16024865,2	K562	blood:

Variant related genes	Relation type
ENSG00000150456	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10451230	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1075901	0.83[EUR][1000 genomes]
rs10852833	0.83[EUR][1000 genomes]
rs11078327	0.82[EUR][1000 genomes]
rs11078331	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078332	0.83[EUR][1000 genomes]
rs1160109	0.80[EUR][1000 genomes]
rs11650678	0.83[EUR][1000 genomes]
rs11652025	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11655773	0.81[EUR][1000 genomes]
rs11656046	0.83[EUR][1000 genomes]
rs11657160	0.83[EUR][1000 genomes]
rs11870608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150017	0.83[EUR][1000 genomes]
rs12449895	0.82[EUR][1000 genomes]
rs178653	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs178654	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178810	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178814	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs178815	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs178818	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs178821	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178822	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178824	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178825	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178826	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178827	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178828	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178831	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs178833	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178835	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178836	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178838	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178839	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1972503	0.80[EUR][1000 genomes]
rs1989856	0.80[EUR][1000 genomes]
rs2078050	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2157990	0.83[EUR][1000 genomes]
rs2157991	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2285579	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285580	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2285582	0.83[EUR][1000 genomes]
rs2285583	0.81[EUR][1000 genomes]
rs2324141	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2324142	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2875265	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35168566	0.83[EUR][1000 genomes]
rs35375077	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3760293	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3785628	0.83[EUR][1000 genomes]
rs4435297	0.80[EUR][1000 genomes]
rs4566208	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4792716	0.83[EUR][1000 genomes]
rs4792717	0.83[EUR][1000 genomes]
rs4792718	0.80[EUR][1000 genomes]
rs4792721	0.83[EUR][1000 genomes]
rs55844265	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502482	0.81[EUR][1000 genomes]
rs6502488	0.83[EUR][1000 genomes]
rs6502490	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6502491	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207463	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7222886	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7223346	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8064702	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8065190	0.83[EUR][1000 genomes]
rs8079969	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8080221	0.80[EUR][1000 genomes]
rs8081406	0.82[EUR][1000 genomes]
rs8081667	0.83[EUR][1000 genomes]
rs9652827	0.83[EUR][1000 genomes]
rs9709250	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9891646	0.80[EUR][1000 genomes]
rs9896441	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9897388	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9902141	0.80[EUR][1000 genomes]
rs9905225	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9907273	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9908591	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9909697	0.81[EUR][1000 genomes]
rs9916868	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
5	nsv907706	chr17:15731923-16056442	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
7	nsv1062220	chr17:15869557-16093156	Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1064878	chr17:15869557-16097241	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv1055173	chr17:15875935-16097241	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1056157	chr17:15890584-16088473	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv833377	chr17:15912013-16104515	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv522169	chr17:15923709-16147821	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv907711	chr17:15978663-16092902	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv907712	chr17:15981874-16103426	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv907713	chr17:15981874-16127206	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	nsv907714	chr17:15990013-16110384	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11658564	ADORA2B	cis	Thyroid	GTEx
rs11658564	ADORA2B	cis	lung	GTEx
rs11658564	ADORA2B	cis	Nerve Tibial	GTEx
rs11658564	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs11658564	ADORA2B	cis	Esophagus Muscularis	GTEx
rs11658564	CENPV	cis	Artery Tibial	GTEx
rs11658564	ADORA2B	cis	Muscle Skeletal	GTEx
rs11658564	ZSWIM7	cis	Muscle Skeletal	GTEx
rs11658564	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs11658564	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs11658564	ADORA2B	cis	Artery Tibial	GTEx
rs11658564	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15999400-16052400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:15999800-16047600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:16005000-16038600	Weak transcription	Stomach Mucosa	stomach
4	chr17:16006600-16064200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr17:16014400-16029800	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:16014600-16028600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:16015400-16030400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:16015400-16031800	Strong transcription	Fetal Intestine Large	intestine
9	chr17:16015600-16077600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr17:16015800-16024600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:16015800-16029600	Strong transcription	Fetal Thymus	thymus
12	chr17:16015800-16064400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr17:16016000-16026600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr17:16016400-16029800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr17:16016400-16064200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr17:16016600-16024400	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr17:16016800-16025200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr17:16016800-16048800	Strong transcription	Adipose Nuclei	Adipose
19	chr17:16017000-16039600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:16017200-16025800	Strong transcription	Fetal Kidney	kidney
21	chr17:16017200-16030400	Strong transcription	Osteobl	bone
22	chr17:16017200-16064200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:16017400-16024600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:16017400-16025000	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr17:16017600-16024600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:16017600-16026400	Strong transcription	Left Ventricle	heart
27	chr17:16017600-16028000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr17:16017600-16036000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:16017800-16024000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:16017800-16025000	Strong transcription	Rectal Smooth Muscle	rectum
31	chr17:16017800-16025400	Strong transcription	HUVEC	blood vessel
32	chr17:16018000-16024400	Strong transcription	HSMM	muscle
33	chr17:16018000-16024600	Strong transcription	NHDF-Ad	bronchial
34	chr17:16018000-16026600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:16018000-16028000	Strong transcription	HepG2	liver
36	chr17:16018200-16025200	Weak transcription	Fetal Heart	heart
37	chr17:16018200-16025600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:16018600-16025600	Strong transcription	Placenta	Placenta
39	chr17:16018600-16033800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:16018600-16037600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr17:16018600-16037600	Weak transcription	Right Ventricle	heart
42	chr17:16018600-16054600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr17:16018800-16025200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr17:16018800-16029800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr17:16018800-16032600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:16019200-16024200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr17:16019200-16025600	Strong transcription	NH-A	brain
48	chr17:16019400-16024600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:16019400-16024600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:16019400-16025000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links