Variant report

Variant	rs12916485
Chromosome Location	chr15:41112142-41112143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10152371	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070294	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070295	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070296	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070297	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856866	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11858010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12148058	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899910	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905621	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12909824	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12916535	0.86[EUR][1000 genomes]
rs17657877	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17657986	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34143869	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34817886	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34948298	0.91[EUR][1000 genomes]
rs35458726	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35621205	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35853942	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736286	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743033	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743034	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4402538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56886112	0.87[EUR][1000 genomes]
rs57818172	0.87[EUR][1000 genomes]
rs57825040	0.87[EUR][1000 genomes]
rs57943888	0.87[EUR][1000 genomes]
rs57994257	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62018585	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492967	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs745032	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036842	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8037830	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12916485	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12916485	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12916485	ZFYVE19	cis	Artery Tibial	GTEx
rs12916485	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12916485	ZFYVE19	cis	Nerve Tibial	GTEx
rs12916485	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12916485	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs12916485	C15orf57	cis	Artery Tibial	GTEx
rs12916485	ZFYVE19	cis	Thyroid	GTEx
rs12916485	ZFYVE19	cis	Artery Aorta	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41100800-41120200	Weak transcription	Small Intestine	intestine
2	chr15:41101400-41115800	Weak transcription	A549	lung
3	chr15:41103800-41115600	Weak transcription	HepG2	liver
4	chr15:41104200-41115800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:41104600-41115800	Weak transcription	HMEC	breast
6	chr15:41106000-41117600	Weak transcription	Hela-S3	cervix
7	chr15:41107200-41135200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:41107400-41115400	Weak transcription	Fetal Intestine Large	intestine
9	chr15:41107400-41118000	Weak transcription	Gastric	stomach
10	chr15:41107600-41117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:41107600-41117600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:41107600-41120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:41107600-41135200	Weak transcription	Esophagus	oesophagus
14	chr15:41107800-41115800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:41107800-41116000	Weak transcription	NHEK	skin
16	chr15:41108200-41115600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:41108200-41135600	Weak transcription	Spleen	Spleen
18	chr15:41108400-41115800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:41108600-41117000	Weak transcription	Colonic Mucosa	Colon
20	chr15:41108600-41117800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:41109000-41117000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:41109200-41120200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:41109600-41116000	Weak transcription	Fetal Intestine Small	intestine
24	chr15:41112000-41135800	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links