Variant report

Variant	rs3786038
Chromosome Location	chr17:19577408-19577409
allele	A/C
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

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1004490	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1004491	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1034897	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204407	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601634	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12602112	0.81[CHD][hapmap]
rs12604069	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12940877	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12945345	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16960251	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1800869	0.84[CHD][hapmap]
rs2072331	0.82[CHD][hapmap]
rs2072332	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2120271	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2386144	0.84[CHD][hapmap]
rs28672254	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2891951	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35364675	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244600	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4621031	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4646793	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646798	0.84[CHD][hapmap]
rs4646800	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924788	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4924791	0.84[ASN][1000 genomes]
rs4925002	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925026	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925037	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925038	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925040	0.88[ASN][1000 genomes]
rs4925041	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56262978	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58970893	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61631401	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68066777	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7215	0.92[YRI][hapmap]
rs73981559	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7502080	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7503517	0.84[CHD][hapmap]
rs758427	0.81[GIH][hapmap]
rs962801	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs968012	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9902636	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9909886	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9914765	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3786038	ALDH3A2	cis	multi-tissue	Pritchard
rs3786038	TRPV2	cis	cerebellum	SCAN
rs3786038	ALDH3A2	cis	cerebellum	SCAN
rs3786038	MFAP4	cis	parietal	SCAN
rs3786038	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs3786038	TOM1L2	cis	parietal	SCAN
rs3786038	ALDH3A2	cis	lymphoblastoid	seeQTL

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	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
5	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
8	chr17:19567600-19578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:19567800-19578600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
13	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:19569600-19578600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr17:19569600-19579000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:19569600-19584000	Weak transcription	Placenta	Placenta
17	chr17:19569800-19578600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:19569800-19578600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
20	chr17:19570000-19578800	Weak transcription	Colonic Mucosa	Colon
21	chr17:19570000-19579200	Weak transcription	Aorta	Aorta
22	chr17:19572600-19582800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr17:19572800-19580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:19572800-19583000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr17:19574200-19577800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr17:19574200-19579000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr17:19574200-19580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:19574200-19582400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr17:19574400-19578600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:19574600-19577600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr17:19574600-19579000	Weak transcription	Ovary	ovary
32	chr17:19574800-19577600	Enhancers	Stomach Mucosa	stomach
33	chr17:19574800-19577800	Strong transcription	Spleen	Spleen
34	chr17:19574800-19583600	Weak transcription	GM12878-XiMat	blood
35	chr17:19575000-19579000	Weak transcription	Primary B cells from cord blood	blood
36	chr17:19575000-19590200	Weak transcription	Right Ventricle	heart
37	chr17:19575400-19578200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr17:19575400-19579000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:19575400-19579000	Weak transcription	Osteobl	bone
40	chr17:19575400-19579200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:19575400-19585400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr17:19575600-19578600	Weak transcription	Pancreas	Pancrea
43	chr17:19575600-19578800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:19575600-19578800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr17:19575600-19579200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:19575600-19579200	Weak transcription	NHEK	skin
47	chr17:19575600-19580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:19575600-19581800	Weak transcription	Gastric	stomach
49	chr17:19575600-19584000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:19575800-19577600	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links