Variant report

Variant	rs332839
Chromosome Location	chr19:38676042-38676043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPINT2-5	chr19:38675016-38676905	ENSG00000269653.1

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2278429	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2569414	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332840	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332842	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332856	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs332864	0.84[CEU][hapmap]
rs34262882	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111180	0.84[CEU][hapmap]
rs9653105	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9653106	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9941474	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
2	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:38658400-38684800	Weak transcription	HepG2	liver
4	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:38661400-38682600	Weak transcription	Aorta	Aorta
6	chr19:38661800-38682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:38664600-38688600	Weak transcription	NH-A	brain
8	chr19:38664600-38699800	Weak transcription	Brain Substantia Nigra	brain
9	chr19:38665000-38684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38665200-38684200	Weak transcription	HMEC	breast
11	chr19:38666200-38682800	Weak transcription	Right Ventricle	heart
12	chr19:38670800-38677400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:38671000-38676600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr19:38671000-38676800	Strong transcription	Primary T cells from cord blood	blood
15	chr19:38671200-38676800	Strong transcription	Liver	Liver
16	chr19:38671200-38684400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:38671200-38691800	Weak transcription	Brain Angular Gyrus	brain
18	chr19:38671800-38676800	Strong transcription	Primary B cells from cord blood	blood
19	chr19:38671800-38677200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr19:38671800-38692400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr19:38671800-38695600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:38672000-38677800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:38672200-38692800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr19:38672600-38676800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:38672600-38677000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:38672600-38699800	Weak transcription	HUVEC	blood vessel
27	chr19:38672800-38676800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:38672800-38693400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:38673000-38676600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr19:38673000-38676800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:38673000-38676800	Strong transcription	A549	lung
32	chr19:38673200-38676400	Strong transcription	Lung	lung
33	chr19:38673200-38676800	Strong transcription	Gastric	stomach
34	chr19:38673200-38676800	Strong transcription	Spleen	Spleen
35	chr19:38673800-38682800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:38673800-38688800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr19:38674000-38677800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:38674400-38676200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:38674400-38676200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:38674400-38676800	Strong transcription	Fetal Intestine Large	intestine
41	chr19:38674400-38676800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:38674400-38682800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:38674400-38696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:38674600-38676800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:38674600-38681800	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:38674600-38691600	Weak transcription	Psoas Muscle	Psoas
47	chr19:38674600-38696800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:38674600-38698600	Strong transcription	Fetal Intestine Small	intestine
49	chr19:38674800-38676400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:38674800-38676400	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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