Variant report

Variant	rs7216
Chromosome Location	chr17:19578873-19578874
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC115989.1.1-6	chr17:19577397-19580908	NONHSAT146517
2	lnc-AC115989.1.1-6	chr17:19578871-19579193	NONHSAT146516

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11204408	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11656199	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11656773	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11871420	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12150145	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12941194	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17684040	0.90[EUR][1000 genomes]
rs1812051	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2108970	0.80[AMR][1000 genomes]
rs2108971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120274	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2159291	0.81[AMR][1000 genomes]
rs2165895	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2245639	0.90[EUR][1000 genomes]
rs2386141	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386142	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440162	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2453586	0.90[EUR][1000 genomes]
rs2453600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2453601	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453604	0.90[EUR][1000 genomes]
rs2453608	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28495827	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28537694	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760489	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4273101	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109259	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62065943	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62065946	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6587200	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6587201	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7210433	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7215	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7405861	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7405862	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7502992	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8069478	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074500	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8074784	0.83[EUR][1000 genomes]
rs8079648	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8081130	1.00[JPT][hapmap];0.80[YRI][hapmap]
rs962800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889632	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9903027	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7216	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
4	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
6	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
9	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:19569600-19579000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:19569600-19584000	Weak transcription	Placenta	Placenta
12	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
13	chr17:19570000-19579200	Weak transcription	Aorta	Aorta
14	chr17:19572600-19582800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr17:19572800-19580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19572800-19583000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr17:19574200-19579000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr17:19574200-19580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:19574200-19582400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:19574600-19579000	Weak transcription	Ovary	ovary
21	chr17:19574800-19583600	Weak transcription	GM12878-XiMat	blood
22	chr17:19575000-19579000	Weak transcription	Primary B cells from cord blood	blood
23	chr17:19575000-19590200	Weak transcription	Right Ventricle	heart
24	chr17:19575400-19579000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:19575400-19579000	Weak transcription	Osteobl	bone
26	chr17:19575400-19579200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr17:19575400-19585400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr17:19575600-19579200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:19575600-19579200	Weak transcription	NHEK	skin
30	chr17:19575600-19580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr17:19575600-19581800	Weak transcription	Gastric	stomach
32	chr17:19575600-19584000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:19575800-19579000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:19575800-19579000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:19575800-19579000	Weak transcription	Hela-S3	cervix
36	chr17:19575800-19579000	Weak transcription	HMEC	breast
37	chr17:19575800-19579200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:19575800-19579600	Weak transcription	Lung	lung
39	chr17:19575800-19583000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr17:19575800-19584600	Weak transcription	HSMM	muscle
41	chr17:19575800-19586600	Weak transcription	Colon Smooth Muscle	Colon
42	chr17:19576000-19579000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:19576000-19579000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:19576000-19579200	Strong transcription	A549	lung
45	chr17:19576000-19579800	Strong transcription	Brain Anterior Caudate	brain
46	chr17:19576000-19580800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr17:19576000-19582200	Weak transcription	HSMMtube	muscle
48	chr17:19576000-19584600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:19576000-19596200	Weak transcription	Fetal Heart	heart
50	chr17:19576200-19579000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links