Variant report

Variant	rs4239134
Chromosome Location	chr17:15883967-15883968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr17:15883767-15884802	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ZSWIM7	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10491104	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1065822	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1079533	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11078321	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11078328	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11078330	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1125156	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11651290	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11651508	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11657912	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11868809	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11869563	0.80[EUR][1000 genomes]
rs11871961	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11872032	0.83[EUR][1000 genomes]
rs12451075	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12942295	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12945546	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12947205	0.90[EUR][1000 genomes]
rs12948361	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2015353	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041459	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2041460	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2051736	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2157992	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286796	0.80[EUR][1000 genomes]
rs2324084	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2779211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34236618	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36001065	0.80[EUR][1000 genomes]
rs3760298	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3785631	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3785633	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815038	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815039	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3826360	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4791660	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4791661	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4791662	0.83[EUR][1000 genomes]
rs4792711	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4792719	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55676330	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62073587	0.81[EUR][1000 genomes]
rs6502482	0.81[EUR][1000 genomes]
rs7207889	0.83[EUR][1000 genomes]
rs7214891	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7217614	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72833498	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs758853	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8070859	0.80[EUR][1000 genomes]
rs8076669	0.83[EUR][1000 genomes]
rs8076864	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8080706	0.91[EUR][1000 genomes]
rs9652828	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9889745	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9889822	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9890012	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9891379	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9898313	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9899002	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9905429	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9908031	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9909615	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][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	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4239134	CENPV	cis	Artery Tibial	GTEx
rs4239134	ADORA2B	cis	Muscle Skeletal	GTEx
rs4239134	ADORA2B	cis	Thyroid	GTEx
rs4239134	ADORA2B	cis	Artery Tibial	GTEx
rs4239134	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs4239134	ADORA2B	cis	Esophagus Muscularis	GTEx
rs4239134	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs4239134	ZSWIM7	cis	Muscle Skeletal	GTEx
rs4239134	ADORA2B	cis	Nerve Tibial	GTEx
rs4239134	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs4239134	NCOR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15870400-15902400	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	chr17:15875200-15884200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:15876600-15885400	Weak transcription	Hela-S3	cervix
7	chr17:15877600-15888800	Weak transcription	NHDF-Ad	bronchial
8	chr17:15877800-15891200	Strong transcription	Fetal Muscle Leg	muscle
9	chr17:15878200-15901800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:15879000-15884600	Weak transcription	NH-A	brain
11	chr17:15879600-15891600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr17:15880200-15901600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:15881200-15892800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:15881400-15901800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr17:15881600-15885400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr17:15881800-15888000	Weak transcription	HepG2	liver
17	chr17:15882000-15884200	Weak transcription	Fetal Intestine Small	intestine
18	chr17:15882200-15884000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:15882200-15884000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr17:15882200-15884200	Weak transcription	HUVEC	blood vessel
21	chr17:15882200-15884400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:15882200-15884800	Weak transcription	Lung	lung
23	chr17:15882200-15885400	Weak transcription	HSMMtube	muscle
24	chr17:15882200-15887600	Weak transcription	Aorta	Aorta
25	chr17:15883200-15884400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr17:15883200-15884600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:15883200-15884600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:15883200-15885000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr17:15883200-15885400	Strong transcription	Fetal Brain Female	brain
30	chr17:15883200-15891200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:15883200-15894000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:15883400-15884000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr17:15883400-15884000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
34	chr17:15883400-15884200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:15883400-15884200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:15883400-15884400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:15883400-15884600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:15883400-15886200	Strong transcription	Brain Germinal Matrix	brain
39	chr17:15883400-15894400	Strong transcription	Fetal Stomach	stomach
40	chr17:15883400-15896600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr17:15883600-15884000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr17:15883600-15884000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:15883600-15884000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr17:15883600-15884000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr17:15883600-15884000	Strong transcription	Primary T cells from cord blood	blood
46	chr17:15883600-15884200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
47	chr17:15883600-15884200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
48	chr17:15883600-15884200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
49	chr17:15883600-15884200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr17:15883600-15884200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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