Variant report

Variant	rs11655456
Chromosome Location	chr17:15894789-15894790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15874769..15877467-chr17:15893088..15895547,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170425	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1045599	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1065822	0.81[EUR][1000 genomes]
rs1075901	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1079533	0.81[EUR][1000 genomes]
rs11078320	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078327	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11078328	0.81[EUR][1000 genomes]
rs11078331	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11651290	0.81[EUR][1000 genomes]
rs11651508	0.80[EUR][1000 genomes]
rs11652025	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11654	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11656046	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11657160	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11657912	0.81[EUR][1000 genomes]
rs11869450	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11869563	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12451075	0.82[EUR][1000 genomes]
rs12942295	0.81[EUR][1000 genomes]
rs12945463	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12945546	0.81[EUR][1000 genomes]
rs1860643	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1860644	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860645	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2041459	0.81[EUR][1000 genomes]
rs2041460	0.81[EUR][1000 genomes]
rs2078050	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109632	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2157990	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2157991	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2157992	0.81[EUR][1000 genomes]
rs2159643	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2285580	0.85[EUR][1000 genomes]
rs2285582	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2285583	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2286795	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286796	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2324084	0.81[EUR][1000 genomes]
rs2535614	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2779207	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2779208	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2779210	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2779212	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35168566	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3760297	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760298	0.82[EUR][1000 genomes]
rs3785628	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3785629	0.88[EUR][1000 genomes]
rs3785631	0.81[EUR][1000 genomes]
rs3785632	0.84[EUR][1000 genomes]
rs3785633	0.82[EUR][1000 genomes]
rs3815038	0.81[EUR][1000 genomes]
rs3815039	0.81[EUR][1000 genomes]
rs3826360	0.83[EUR][1000 genomes]
rs4435297	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4792707	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4792708	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4792709	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4792711	0.81[EUR][1000 genomes]
rs4792712	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4792713	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4792715	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4792716	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4792717	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4792718	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792719	0.81[EUR][1000 genomes]
rs6416868	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502479	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6502480	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6502482	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502488	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7207463	0.84[EUR][1000 genomes]
rs7209094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7210655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7214695	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7214891	0.81[EUR][1000 genomes]
rs7216949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7222886	0.80[EUR][1000 genomes]
rs7223346	0.92[EUR][1000 genomes]
rs758853	0.81[EUR][1000 genomes]
rs8064702	0.92[EUR][1000 genomes]
rs8065190	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8066902	0.81[EUR][1000 genomes]
rs8070859	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8075345	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8076669	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8076864	0.81[EUR][1000 genomes]
rs8080221	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8081406	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8081667	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9652827	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9652828	0.81[EUR][1000 genomes]
rs9709250	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9889822	0.81[EUR][1000 genomes]
rs9890012	0.81[EUR][1000 genomes]
rs9891379	0.81[EUR][1000 genomes]
rs9891938	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896441	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9897542	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9899002	0.82[EUR][1000 genomes]
rs9899995	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9907273	0.80[EUR][1000 genomes]
rs9908031	0.81[EUR][1000 genomes]
rs9909615	0.81[EUR][1000 genomes]
rs9916868	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	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
7	nsv1067555	chr17:15804228-16001117	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	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
9	nsv907707	chr17:15846535-15950751	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv907709	chr17:15851196-15937487	Weak transcription Genic enhancers Strong transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
11	nsv907708	chr17:15851196-15950751	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
12	nsv1057493	chr17:15852125-15930718	Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv543215	chr17:15852125-15930718	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv907710	chr17:15854257-15950751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11655456	CENPV	cis	Artery Tibial	GTEx
rs11655456	ADORA2B	cis	Esophagus Muscularis	GTEx
rs11655456	ADORA2B	cis	lung	GTEx
rs11655456	ZSWIM7	cis	Muscle Skeletal	GTEx
rs11655456	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs11655456	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs11655456	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs11655456	ADORA2B	cis	Nerve Tibial	GTEx
rs11655456	ADORA2B	cis	Muscle Skeletal	GTEx
rs11655456	ADORA2B	cis	Artery Tibial	GTEx
rs11655456	ADORA2B	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15870400-15902400	Weak transcription	Small Intestine	intestine
2	chr17:15870800-15902400	Weak transcription	Esophagus	oesophagus
3	chr17:15873200-15902200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:15874800-15902400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:15878200-15901800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:15880200-15901600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:15881400-15901800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:15883400-15896600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr17:15883600-15895200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:15883600-15895400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:15883600-15896600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:15883600-15898000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:15883600-15898400	Strong transcription	Liver	Liver
14	chr17:15884000-15901600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:15884000-15902200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:15884400-15902000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr17:15884600-15898600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:15884600-15901600	Weak transcription	Fetal Kidney	kidney
19	chr17:15884600-15901600	Weak transcription	NHLF	lung
20	chr17:15884600-15902000	Weak transcription	Fetal Brain Male	brain
21	chr17:15884600-15902400	Weak transcription	Gastric	stomach
22	chr17:15884800-15902000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr17:15885000-15902000	Weak transcription	Psoas Muscle	Psoas
24	chr17:15885600-15902000	Weak transcription	Colonic Mucosa	Colon
25	chr17:15885600-15902400	Weak transcription	Lung	lung
26	chr17:15885800-15902000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:15886000-15894800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr17:15886000-15900800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:15886000-15901200	Strong transcription	Fetal Intestine Small	intestine
30	chr17:15886200-15901800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr17:15886200-15902200	Weak transcription	Pancreas	Pancrea
32	chr17:15887000-15896400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr17:15887200-15894800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:15887200-15896600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:15887200-15897800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:15887200-15897800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:15887400-15898800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:15887800-15895000	Strong transcription	Placenta	Placenta
39	chr17:15888000-15901400	Weak transcription	Hela-S3	cervix
40	chr17:15888200-15901000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr17:15888400-15895800	Weak transcription	HUVEC	blood vessel
42	chr17:15888400-15901400	Weak transcription	Brain Angular Gyrus	brain
43	chr17:15888400-15901400	Weak transcription	Colon Smooth Muscle	Colon
44	chr17:15888400-15902400	Weak transcription	Spleen	Spleen
45	chr17:15888600-15901800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:15889000-15899000	Weak transcription	Fetal Heart	heart
47	chr17:15889200-15896000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:15889200-15899000	Weak transcription	NHDF-Ad	bronchial
49	chr17:15889200-15901600	Weak transcription	HSMM	muscle
50	chr17:15889400-15897800	Weak transcription	NHEK	skin

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