Variant report

Variant	rs10403273
Chromosome Location	chr19:19372968-19372969
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19372960-19373009	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr19:19371722-19373720	H1-hESC	embryonic stem cell:	n/a	chr19:19372494-19372508 chr19:19372658-19372671
3	SP1	chr19:19372412-19372990	H1-hESC	embryonic stem cell:	n/a	chr19:19372576-19372588 chr19:19372643-19372652 chr19:19372559-19372569 chr19:19372578-19372587 chr19:19372681-19372692 chr19:19372642-19372654 chr19:19372576-19372588 chr19:19372642-19372654 chr19:19372682-19372691 chr19:19372644-19372657 chr19:19372577-19372591 chr19:19372643-19372653 chr19:19372643-19372652 chr19:19372644-19372653 chr19:19372643-19372657 chr19:19372643-19372653
4	EGR1	chr19:19372605-19373027	H1-hESC	embryonic stem cell:	n/a	chr19:19372643-19372653 chr19:19372612-19372622
5	YY1	chr19:19372565-19373525	H1-hESC	embryonic stem cell:	n/a	chr19:19372575-19372584 chr19:19372644-19372653
6	CTBP2	chr19:19371708-19373865	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr19:19372333-19373808	H1-hESC	embryonic stem cell:	n/a	chr19:19373516-19373526

No.	Distal block	Cell Line	Cell type
1	chr19:19371179..19375166-chr19:19377084..19380673,3	K562	blood:
2	chr19:19371281..19373352-chr19:19383019..19385169,2	K562	blood:
3	chr19:19371873..19374134-chr19:19452929..19454746,2	K562	blood:
4	chr19:19370401..19373352-chr19:19382111..19385169,3	K562	blood:

Variant related genes	Relation type
HAPLN4	TF binding region
ENSG00000267629	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000213996	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10401714	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10407933	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414990	0.83[ASN][1000 genomes]
rs10417330	0.81[ASN][1000 genomes]
rs10422893	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423659	0.81[ASN][1000 genomes]
rs10423874	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1064395	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11555053	0.92[EUR][1000 genomes]
rs1557723	0.81[EUR][1000 genomes]
rs17216041	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17751061	0.89[EUR][1000 genomes]
rs1989867	0.81[EUR][1000 genomes]
rs2010506	0.96[EUR][1000 genomes]
rs2011503	0.81[EUR][1000 genomes]
rs2074295	0.87[AFR][1000 genomes]
rs2074302	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2315023	0.90[EUR][1000 genomes]
rs35854118	0.96[EUR][1000 genomes]
rs3752170	0.81[ASN][1000 genomes]
rs4239639	0.83[EUR][1000 genomes]
rs4563151	0.81[ASN][1000 genomes]
rs4808932	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808933	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808934	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808944	0.90[EUR][1000 genomes]
rs55762233	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55765017	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55822665	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56044734	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56135441	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56144632	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56212061	0.84[EUR][1000 genomes]
rs56278919	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57436187	0.88[EUR][1000 genomes]
rs6511027	0.93[EUR][1000 genomes]
rs7257875	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72999030	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72999059	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72999063	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72999068	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs756999	0.81[EUR][1000 genomes]
rs8100097	0.82[EUR][1000 genomes]
rs8108777	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998732	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active 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	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911306	chr19:19366643-19391838	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10403273	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19371400-19373000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
2	chr19:19371400-19374000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:19371400-19374000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:19371400-19374000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:19371600-19373000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:19371600-19373000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr19:19371600-19373400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
8	chr19:19371600-19374000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:19371800-19373000	Bivalent/Poised TSS	Right Ventricle	heart
10	chr19:19371800-19373200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr19:19371800-19373400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:19371800-19373600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr19:19371800-19374000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
14	chr19:19371800-19374200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:19372000-19373000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:19372000-19373200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:19372000-19373200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
18	chr19:19372000-19373400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr19:19372000-19373800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr19:19372200-19373000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:19372200-19373000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:19372200-19373000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:19372200-19373000	Enhancers	Pancreas	Pancrea
24	chr19:19372200-19373000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr19:19372200-19373200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:19372400-19373000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr19:19372400-19373000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
28	chr19:19372400-19373200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:19372400-19373200	Active TSS	Brain Anterior Caudate	brain
30	chr19:19372400-19373400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:19372400-19373600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
32	chr19:19372600-19373200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:19372600-19373200	Bivalent Enhancer	Colonic Mucosa	Colon
34	chr19:19372600-19373400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr19:19372600-19373400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:19372600-19373800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr19:19372600-19373800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:19372800-19373000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:19372800-19373000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:19372800-19373000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr19:19372800-19373000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:19372800-19373000	Bivalent Enhancer	Brain Hippocampus Middle	brain
43	chr19:19372800-19373000	Bivalent Enhancer	Fetal Brain Male	brain
44	chr19:19372800-19373000	Bivalent/Poised TSS	Fetal Lung	lung
45	chr19:19372800-19373000	Bivalent Enhancer	Stomach Mucosa	stomach
46	chr19:19372800-19373000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr19:19372800-19373200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:19372800-19373200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr19:19372800-19373200	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr19:19372800-19373200	Bivalent Enhancer	Brain Substantia Nigra	brain

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