Variant report

Variant	rs62120388
Chromosome Location	chr19:18316961-18316962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr19:18316884-18316964	K562	blood:	n/a	n/a
2	POLR2A	chr19:18313917-18317009	IMR90	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18312530..18316975-chr19:18331566..18338113,9	K562	blood:
2	chr19:18312530..18319182-chr19:18329520..18338113,19	K562	blood:
3	chr19:18313916..18318092-chr19:18528402..18531529,5	K562	blood:
4	chr19:18314296..18317431-chr19:18383748..18386421,3	K562	blood:
5	chr19:18314746..18317215-chr19:18546753..18549806,3	K562	blood:
6	chr19:18314629..18316965-chr19:18497132..18498761,2	K562	blood:
7	chr19:18302289..18309850-chr19:18311214..18320810,23	K562	blood:
8	chr19:18316952..18321677-chr19:18390588..18394858,6	K562	blood:
9	chr19:18314296..18317366-chr19:18383748..18385809,3	K562	blood:
10	chr19:18315560..18317882-chr19:18321449..18323321,2	K562	blood:

No data

Variant related genes	Relation type
RAB3A	TF binding region
ENSG00000130513	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000105650	Chromatin interaction
ENSG00000130518	Chromatin interaction
ENSG00000264175	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1046565	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11881258	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12460619	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461021	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462801	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17683509	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17683539	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2229228	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3803919	0.95[EUR][1000 genomes]
rs4458132	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808768	0.92[EUR][1000 genomes]
rs55650549	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120367	0.85[EUR][1000 genomes]
rs62120368	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120382	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120383	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62120385	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62120393	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6512247	0.83[ASN][1000 genomes]
rs7245576	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7246274	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7259695	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8100626	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8104010	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109807	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	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
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer 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	136 gene(s)	inside rSNPs	diseases
11	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
13	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
14	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
15	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	nsv911263	chr19:18309365-18324329	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv911264	chr19:18309365-18369644	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18313600-18317000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:18314000-18317000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr19:18314200-18317200	Active TSS	Fetal Brain Female	brain
4	chr19:18314400-18317000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:18314400-18317600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:18314600-18317000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:18314800-18321000	Weak transcription	Spleen	Spleen
8	chr19:18316200-18317000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:18316200-18317000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:18316200-18317000	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr19:18316200-18317000	Enhancers	Lung	lung
12	chr19:18316200-18335000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:18316400-18317000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:18316400-18317000	Bivalent Enhancer	Fetal Thymus	thymus
15	chr19:18316400-18317200	Enhancers	Primary hematopoietic stem cells	blood
16	chr19:18316400-18317200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:18316400-18319000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:18316600-18317000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:18316600-18317000	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:18316600-18317000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr19:18316600-18317000	Enhancers	Brain Cingulate Gyrus	brain
22	chr19:18316600-18317000	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr19:18316600-18317000	Enhancers	Placenta	Placenta
24	chr19:18316600-18317000	Enhancers	Dnd41	blood
25	chr19:18316600-18317000	Enhancers	NH-A	brain
26	chr19:18316600-18317000	Enhancers	NHDF-Ad	bronchial
27	chr19:18316600-18317200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:18316600-18317200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:18316600-18317200	Enhancers	Fetal Brain Male	brain
30	chr19:18316600-18317200	Enhancers	Fetal Intestine Large	intestine
31	chr19:18316600-18317200	Enhancers	Fetal Kidney	kidney
32	chr19:18316600-18317200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr19:18316600-18317400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:18316600-18317800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:18316600-18318600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:18316600-18318600	Weak transcription	HSMM	muscle
37	chr19:18316600-18318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:18316600-18318800	Weak transcription	A549	lung
39	chr19:18316600-18318800	Weak transcription	HSMMtube	muscle
40	chr19:18316600-18319000	Enhancers	Fetal Stomach	stomach
41	chr19:18316600-18319000	Weak transcription	Stomach Mucosa	stomach
42	chr19:18316600-18319000	Weak transcription	Hela-S3	cervix
43	chr19:18316600-18319200	Weak transcription	Right Atrium	heart
44	chr19:18316600-18325800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr19:18316600-18331200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:18316800-18317000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:18316800-18317000	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr19:18316800-18317000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr19:18316800-18317000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:18316800-18317000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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