Variant report

Variant	rs4803862
Chromosome Location	chr19:38693305-38693306
allele	A/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	chr19:38693298-38693358	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38692307..38694254-chr19:38695485..38698423,2	K562	blood:
2	chr19:38688847..38690715-chr19:38692444..38696318,3	K562	blood:
3	chr19:38687810..38690536-chr19:38691430..38693944,2	K562	blood:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000268499	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10412762	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs10420506	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap]
rs10422665	0.81[CEU][hapmap]
rs1654365	0.81[CHB][hapmap]
rs4802256	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[TSI][hapmap]
rs4802278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803828	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap]
rs4803829	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs73627686	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73930553	0.84[EUR][1000 genomes]
rs855633	0.81[CHB][hapmap]
rs860623	0.81[CHB][hapmap]
rs863020	0.81[CHB][hapmap]
rs941039	0.81[CHB][hapmap]
rs9941467	0.81[CEU][hapmap];0.90[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4803862	CBLC	cis	parietal	SCAN
rs4803862	SIPA1L3	cis	Heart Left Ventricle	GTEx
rs4803862	ZNF234	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
2	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:38664600-38699800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:38671800-38695600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:38672600-38699800	Weak transcription	HUVEC	blood vessel
7	chr19:38672800-38693400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:38674400-38696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:38674600-38696800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:38674600-38698600	Strong transcription	Fetal Intestine Small	intestine
11	chr19:38674800-38696200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:38674800-38696800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:38674800-38697000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:38674800-38699000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:38674800-38699000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:38674800-38700400	Weak transcription	Fetal Kidney	kidney
17	chr19:38675400-38700200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:38675600-38696800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:38675800-38694600	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:38676000-38699800	Weak transcription	Right Atrium	heart
21	chr19:38676400-38693600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:38676800-38698200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:38679400-38699400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr19:38679600-38697800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:38679800-38698400	Strong transcription	Fetal Intestine Large	intestine
26	chr19:38679800-38698600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr19:38680000-38699400	Weak transcription	Dnd41	blood
28	chr19:38680600-38697800	Strong transcription	Fetal Stomach	stomach
29	chr19:38680600-38698000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:38680600-38698400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:38680600-38698600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:38681000-38698200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:38681000-38698400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:38682200-38697800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:38682200-38698400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:38682400-38697800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:38682600-38694800	Strong transcription	Osteobl	bone
38	chr19:38682600-38695200	Strong transcription	Colonic Mucosa	Colon
39	chr19:38682600-38697000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr19:38682600-38697200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:38682600-38698200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:38684800-38697200	Strong transcription	Fetal Muscle Leg	muscle
43	chr19:38685200-38695200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:38685400-38693400	Strong transcription	Spleen	Spleen
45	chr19:38685400-38694200	Weak transcription	Stomach Mucosa	stomach
46	chr19:38685400-38700000	Weak transcription	HMEC	breast
47	chr19:38685400-38713800	Weak transcription	HepG2	liver
48	chr19:38686000-38694400	Strong transcription	A549	lung
49	chr19:38686000-38697600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:38686200-38698000	Weak transcription	Fetal Thymus	thymus

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