Variant report

Variant	rs4479364
Chromosome Location	chr19:40824288-40824289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLD3-3	chr19:40819394-40825438	NONHSAT066371

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11083554	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12151335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12459567	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460555	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12460615	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12977474	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985477	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16974196	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1962639	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1991460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304186	0.82[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2368575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33933140	0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34894858	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs35562135	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745195	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3746006	0.81[JPT][hapmap]
rs4490097	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4502340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4524046	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802072	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4803324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803325	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803327	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55710016	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57158010	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58502633	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59263025	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259273	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7259541	0.85[JPT][hapmap]
rs73046335	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7507651	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508513	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110323	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs890773	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892117	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv3386713	chr19:40794161-40828617	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4479364	ERCC1	cis	parietal	SCAN
rs4479364	PLAUR	cis	cerebellum	SCAN
rs4479364	VASP	cis	cerebellum	SCAN
rs4479364	DMRTC2	cis	parietal	SCAN
rs4479364	TMEM91	cis	parietal	SCAN
rs4479364	MIA	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40792000-40826200	Weak transcription	Hela-S3	cervix
2	chr19:40800400-40826400	Weak transcription	Brain Angular Gyrus	brain
3	chr19:40802800-40828000	Weak transcription	NH-A	brain
4	chr19:40810600-40825800	Weak transcription	Adipose Nuclei	Adipose
5	chr19:40810600-40829800	Weak transcription	NHDF-Ad	bronchial
6	chr19:40810800-40826200	Weak transcription	HMEC	breast
7	chr19:40811200-40826000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:40811400-40826600	Weak transcription	NHEK	skin
9	chr19:40811600-40826600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:40811800-40826400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:40811800-40826600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:40811800-40826600	Weak transcription	Fetal Lung	lung
13	chr19:40811800-40831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:40814600-40824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:40815400-40832800	Weak transcription	Fetal Brain Male	brain
16	chr19:40815600-40826000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:40815800-40824400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:40817200-40825800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:40817400-40827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:40817600-40827200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr19:40819000-40824400	Weak transcription	GM12878-XiMat	blood
22	chr19:40819200-40825800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:40819200-40826800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:40819200-40834000	Weak transcription	Fetal Kidney	kidney
25	chr19:40819400-40824400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:40819400-40828200	Weak transcription	Osteobl	bone
27	chr19:40819800-40826600	Weak transcription	Primary B cells from cord blood	blood
28	chr19:40819800-40826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:40820000-40824400	Weak transcription	Fetal Thymus	thymus
30	chr19:40820000-40827400	Weak transcription	HepG2	liver
31	chr19:40820200-40826400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:40820400-40826000	Weak transcription	Gastric	stomach
33	chr19:40820600-40826600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:40820600-40827400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:40820800-40825800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:40820800-40825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:40820800-40825800	Weak transcription	Esophagus	oesophagus
38	chr19:40820800-40825800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr19:40820800-40826000	Weak transcription	Fetal Intestine Large	intestine
40	chr19:40820800-40826600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:40820800-40848400	Strong transcription	Dnd41	blood
42	chr19:40821000-40825200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:40821000-40825800	Weak transcription	HSMM	muscle
44	chr19:40821000-40826000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:40821200-40826000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:40821200-40831800	Weak transcription	K562	blood
47	chr19:40821400-40827200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:40821400-40827800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:40821400-40835000	Strong transcription	Fetal Intestine Small	intestine
50	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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