Variant report

Variant	rs4803369
Chromosome Location	chr19:41315980-41315981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41222253..41224407-chr19:41315424..41318276,2	K562	blood:
2	chr19:41221543..41224231-chr19:41314588..41316621,2	MCF-7	breast:
3	chr19:41221999..41223753-chr19:41315424..41317151,2	K562	blood:
4	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
5	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
6	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:

Variant related genes	Relation type
ENSG00000167578	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11547373	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880960	1.00[LWK][hapmap]
rs12052092	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12151282	0.91[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12973666	0.82[JPT][hapmap]
rs17726276	0.82[JPT][hapmap]
rs2279011	0.82[JPT][hapmap]
rs2305797	0.87[ASW][hapmap];0.84[CEU][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs35061187	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35405967	0.95[ASN][1000 genomes]
rs35858034	0.82[EUR][1000 genomes]
rs3733829	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776611	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41530251	0.84[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4802090	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802091	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245595	0.87[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs73048928	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4803369	CIC	cis	parietal	SCAN
rs4803369	RPS19	cis	parietal	SCAN
rs4803369	KCNN4	cis	cerebellum	SCAN
rs4803369	DMPK	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41305800-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41306400-41316200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:41308400-41316400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:41309000-41316200	Genic enhancers	Placenta	Placenta
6	chr19:41309400-41316000	Genic enhancers	Spleen	Spleen
7	chr19:41309800-41316200	Genic enhancers	Lung	lung
8	chr19:41309800-41316400	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr19:41311200-41316400	Strong transcription	Dnd41	blood
10	chr19:41312400-41316000	Weak transcription	Small Intestine	intestine
11	chr19:41312800-41316000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:41313000-41316000	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr19:41313000-41316400	Weak transcription	Fetal Kidney	kidney
14	chr19:41313200-41316000	Weak transcription	Fetal Heart	heart
15	chr19:41313400-41316000	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr19:41313400-41316000	Strong transcription	NHEK	skin
17	chr19:41313400-41316400	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr19:41313400-41316400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr19:41313600-41316000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:41313600-41316000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:41313600-41316000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:41313600-41316200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:41313600-41316600	Weak transcription	Fetal Brain Male	brain
24	chr19:41313800-41316000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:41313800-41316000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:41313800-41316000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:41313800-41316000	Strong transcription	Fetal Thymus	thymus
28	chr19:41313800-41316000	Weak transcription	HSMMtube	muscle
29	chr19:41314000-41316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr19:41314200-41316000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:41314200-41316200	Strong transcription	Brain Germinal Matrix	brain
32	chr19:41314600-41316000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr19:41314600-41316200	Weak transcription	Stomach Mucosa	stomach
34	chr19:41314600-41316600	Weak transcription	Hela-S3	cervix
35	chr19:41314800-41316000	Weak transcription	Fetal Lung	lung
36	chr19:41314800-41316200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:41314800-41316200	Weak transcription	Brain Angular Gyrus	brain
38	chr19:41314800-41316600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:41315000-41316000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:41315000-41316000	Weak transcription	NH-A	brain
41	chr19:41315000-41316600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:41315000-41324400	Weak transcription	HepG2	liver
43	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
44	chr19:41315200-41316000	Genic enhancers	Colon Smooth Muscle	Colon
45	chr19:41315200-41316000	Genic enhancers	Esophagus	oesophagus
46	chr19:41315200-41316000	Genic enhancers	Gastric	stomach
47	chr19:41315200-41316000	Genic enhancers	Pancreas	Pancrea
48	chr19:41315200-41316000	Genic enhancers	NHLF	lung
49	chr19:41315200-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:41315200-41316200	Genic enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links