Variant report

Variant	rs4803828
Chromosome Location	chr19:38663860-38663861
allele	A/C
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	chr19:38663718-38664578	U87	brain:	n/a	n/a
2	POLR2A	chr19:38663856-38663899	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:38663756-38664578	U87	brain:	n/a	n/a
4	POLR2A	chr19:38663848-38664116	A549	lung:	n/a	n/a
5	PBX3	chr19:38663858-38664411	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr19:38663727-38664430	SK-N-SH	brain:	n/a	chr19:38664093-38664103
7	PBX3	chr19:38663779-38664389	SK-N-SH	brain:	n/a	n/a
8	GATA2	chr19:38663750-38664066	SH-SY5Y	brain:	n/a	n/a
9	MYC	chr19:38663854-38664506	MCF10A-Er-Src	breast:	n/a	chr19:38664240-38664250 chr19:38664240-38664249 chr19:38664238-38664251 chr19:38664239-38664250 chr19:38664241-38664248 chr19:38664240-38664249 chr19:38664239-38664250 chr19:38664238-38664251 chr19:38664239-38664249
10	FOS	chr19:38663823-38664351	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SIPA1L3	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10401165	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10403716	0.95[ASN][1000 genomes]
rs10412762	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10412865	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10420506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422665	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11083448	0.83[EUR][1000 genomes]
rs1614979	0.81[JPT][hapmap]
rs1654349	0.81[JPT][hapmap]
rs1654365	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1725475	0.81[JPT][hapmap]
rs1725512	0.81[JPT][hapmap]
rs2082442	0.95[ASN][1000 genomes]
rs2082443	0.95[ASN][1000 genomes]
rs28444246	0.95[EUR][1000 genomes]
rs28495744	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28581256	0.92[ASN][1000 genomes]
rs4802233	0.81[JPT][hapmap]
rs4802247	0.93[ASN][1000 genomes]
rs4802256	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802278	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap]
rs4803786	0.88[ASN][1000 genomes]
rs4803809	0.95[ASN][1000 genomes]
rs4803810	0.95[ASN][1000 genomes]
rs4803829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803862	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap]
rs56166457	0.85[ASN][1000 genomes]
rs59185302	0.88[ASN][1000 genomes]
rs59579475	0.85[ASN][1000 genomes]
rs59924887	0.88[ASN][1000 genomes]
rs61388128	0.88[ASN][1000 genomes]
rs6508767	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7245788	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248428	0.91[ASN][1000 genomes]
rs7250034	0.95[ASN][1000 genomes]
rs7256332	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73627654	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73627663	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73627676	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73627686	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73930553	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8105468	0.88[ASN][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.81[JPT][hapmap]
rs855633	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs855636	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs860623	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs863020	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs941039	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs941040	0.81[JPT][hapmap]
rs9941456	0.95[ASN][1000 genomes]
rs9941467	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4803828	RINL	cis	cerebellum	SCAN
rs4803828	SIPA1L3	cis	Heart Left Ventricle	GTEx
rs4803828	BCAM	cis	parietal	SCAN
rs4803828	ZNF234	cis	parietal	SCAN
rs4803828	CBLC	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38653600-38665200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:38653600-38668600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
5	chr19:38653800-38664000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:38653800-38666600	Strong transcription	A549	lung
7	chr19:38653800-38670800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:38654000-38664000	Strong transcription	Fetal Stomach	stomach
9	chr19:38655200-38669400	Weak transcription	Fetal Lung	lung
10	chr19:38656200-38664200	Weak transcription	HSMMtube	muscle
11	chr19:38656200-38664200	Weak transcription	NHDF-Ad	bronchial
12	chr19:38656200-38675200	Weak transcription	Stomach Mucosa	stomach
13	chr19:38656400-38670400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:38656400-38670400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:38656400-38670800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:38656400-38671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:38656400-38674000	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:38656800-38669400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:38657400-38665800	Weak transcription	NHLF	lung
20	chr19:38657600-38673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:38657600-38673800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:38657800-38669600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:38658400-38674000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:38658400-38684800	Weak transcription	HepG2	liver
26	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:38658600-38670800	Weak transcription	Fetal Brain Female	brain
28	chr19:38658800-38669200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:38658800-38669400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:38658800-38669400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:38658800-38670400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr19:38659600-38666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:38659600-38666400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:38659600-38668800	Weak transcription	Primary B cells from cord blood	blood
35	chr19:38659600-38673600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:38659600-38673600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:38659800-38669400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:38659800-38670600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr19:38660400-38669600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:38661000-38669400	Weak transcription	Liver	Liver
41	chr19:38661000-38673200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:38661200-38664000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:38661200-38668800	Weak transcription	Thymus	Thymus
44	chr19:38661200-38669400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38661200-38670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:38661200-38671200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:38661200-38673600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:38661400-38665800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:38661400-38669400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:38661400-38682600	Weak transcription	Aorta	Aorta

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