Variant report

Variant	rs58410315
Chromosome Location	chr19:18554377-18554378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18553947..18555891-chr19:18746913..18749059,2	K562	blood:
2	chr19:18552236..18554463-chr19:18572240..18574871,2	K562	blood:
3	chr19:18389237..18391890-chr19:18553028..18555362,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSBP4-2	chr19:18553935-18555242	NONHSAT062974
2	lnc-ISYNA1-2	chr19:18553705-18554469	NONHSAT062975
3	lnc-SSBP4-2	chr19:18553935-18554407	ENSG00000268199.2

No data

Variant related genes	Relation type
ENSG00000167487	Chromatin interaction
ENSG00000130522	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11574806	0.87[EUR][1000 genomes]
rs16982418	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16982427	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16982429	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16982485	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2314669	0.87[EUR][1000 genomes]
rs34078075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34868531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35328461	1.00[EUR][1000 genomes]
rs58604797	1.00[EUR][1000 genomes]
rs58723610	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58842178	1.00[EUR][1000 genomes]
rs59511380	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59549953	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60687616	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61743938	1.00[EUR][1000 genomes]
rs61743954	0.87[EUR][1000 genomes]
rs7247603	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73523072	0.87[EUR][1000 genomes]
rs73523074	0.87[EUR][1000 genomes]
rs8101976	1.00[EUR][1000 genomes]
rs8102397	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
3	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
7	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
8	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
10	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	esv3401601	chr19:18551998-18554482	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18545200-18570000	Weak transcription	Small Intestine	intestine
2	chr19:18549200-18554400	Weak transcription	Primary B cells from cord blood	blood
3	chr19:18549200-18559600	Weak transcription	HSMM	muscle
4	chr19:18549200-18566200	Weak transcription	HUVEC	blood vessel
5	chr19:18549400-18554600	Weak transcription	Brain Angular Gyrus	brain
6	chr19:18549400-18556400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:18549600-18554400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:18549600-18554400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:18549800-18554600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:18549800-18567000	Weak transcription	Psoas Muscle	Psoas
11	chr19:18550000-18554400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:18550000-18554400	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:18550200-18554400	Weak transcription	Adipose Nuclei	Adipose
14	chr19:18550200-18554600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:18550200-18559600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:18550400-18554400	Weak transcription	Aorta	Aorta
17	chr19:18550400-18554400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:18550400-18557200	Weak transcription	Fetal Lung	lung
19	chr19:18550600-18554600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:18550600-18554600	Weak transcription	Osteobl	bone
21	chr19:18550600-18562000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr19:18550800-18554400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:18550800-18554400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:18550800-18554400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:18550800-18557000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:18550800-18569800	Weak transcription	Right Atrium	heart
27	chr19:18551000-18556600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr19:18551000-18561200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:18551200-18555400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:18551400-18557000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:18551600-18554400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:18551600-18556600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:18551600-18561600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:18551600-18570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:18551800-18556600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:18551800-18561600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr19:18551800-18561800	Strong transcription	Fetal Stomach	stomach
38	chr19:18552200-18554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:18552200-18554400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr19:18552600-18554400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:18552600-18554800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:18552800-18554400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:18552800-18562000	Strong transcription	NHLF	lung
44	chr19:18553000-18554400	Active TSS	Fetal Muscle Trunk	muscle
45	chr19:18553200-18556400	Strong transcription	Colonic Mucosa	Colon
46	chr19:18553200-18558000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:18553400-18554400	Weak transcription	HMEC	breast
48	chr19:18553400-18555000	Weak transcription	HepG2	liver
49	chr19:18553400-18556000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
50	chr19:18553400-18556800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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