Variant report

Variant	rs7258762
Chromosome Location	chr19:51111061-51111062
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:51108915..51112953-chr19:51162682..51166555,5	K562	blood:
2	chr19:51103570..51107800-chr19:51108221..51112163,4	K562	blood:
3	chr19:51109906..51112856-chr19:51294280..51296293,2	K562	blood:
4	chr19:51110056..51112953-chr19:51162682..51165400,3	K562	blood:
5	chr19:51109418..51112998-chr19:51159027..51162201,6	K562	blood:
6	chr19:51109418..51112978-chr19:51159521..51162574,6	K562	blood:

Variant related genes	Relation type
ENSG00000161681	Chromatin interaction
ENSG00000235034	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10426057	0.83[EUR][1000 genomes]
rs16986142	0.83[EUR][1000 genomes]
rs1895373	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1895374	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6509490	0.83[ASN][1000 genomes]
rs7253426	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253669	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1062281	chr19:51053340-51230844	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1062548	chr19:51081358-51230844	Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1065222	chr19:51084705-51136844	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv16242	chr19:51106142-51111826	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3374132	chr19:51108440-51113138	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv828581	chr19:51109572-51124716	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv961234	chr19:51109635-51126366	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv33810	chr19:51110251-51124545	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7258762	SYT3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51110600-51111200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
2	chr19:51110600-51111200	Flanking Active TSS	Brain Substantia Nigra	brain
3	chr19:51110600-51111200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
4	chr19:51110600-51111800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
5	chr19:51110600-51112000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr19:51110600-51112000	ZNF genes & repeats	Spleen	Spleen
7	chr19:51110800-51111200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:51110800-51111200	Flanking Active TSS	Brain Angular Gyrus	brain
9	chr19:51110800-51111200	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr19:51110800-51111200	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr19:51110800-51111200	Bivalent Enhancer	Fetal Heart	heart
12	chr19:51110800-51111400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
13	chr19:51110800-51111400	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr19:51110800-51111400	Bivalent Enhancer	Colonic Mucosa	Colon
15	chr19:51110800-51111400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
16	chr19:51110800-51111600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
17	chr19:51110800-51111600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:51110800-51111800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:51110800-51111800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr19:51110800-51111800	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr19:51110800-51111800	Active TSS	A549	lung
22	chr19:51110800-51112000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:51110800-51112000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr19:51110800-51112000	Enhancers	Primary B cells from peripheral blood	blood
25	chr19:51110800-51112000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr19:51110800-51112200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:51111000-51111200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr19:51111000-51111200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:51111000-51111200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:51111000-51111200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:51111000-51111200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:51111000-51111200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:51111000-51111200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
34	chr19:51111000-51111200	Flanking Active TSS	Fetal Brain Male	brain
35	chr19:51111000-51111200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
36	chr19:51111000-51111200	Flanking Active TSS	K562	blood
37	chr19:51111000-51111400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:51111000-51111400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr19:51111000-51111400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:51111000-51111400	Bivalent Enhancer	Adipose Nuclei	Adipose
41	chr19:51111000-51111600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr19:51111000-51111600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:51111000-51111600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr19:51111000-51111600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr19:51111000-51111600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr19:51111000-51111600	Bivalent Enhancer	Placenta	Placenta
47	chr19:51111000-51111600	Enhancers	Osteobl	bone
48	chr19:51111000-51111800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
49	chr19:51111000-51112000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr19:51111000-51112000	Active TSS	HUES6 Cell Line	embryonic stem cell

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