Variant report

Variant	rs10150333
Chromosome Location	chr14:56597317-56597318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10134875	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11158082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs1117310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs1382973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs173352	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2054491	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2054492	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2086326	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs242412	0.82[TSI][hapmap]
rs242420	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242578	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs3783675	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs3844020	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3912199	0.80[MEX][hapmap]
rs3912200	0.90[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3912201	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143949	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4898882	0.83[TSI][hapmap]
rs4901638	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7140444	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7145330	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7151741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899604	0.91[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10150333	CDKN3	cis	parietal	SCAN
rs10150333	GNPNAT1	cis	cerebellum	SCAN
rs10150333	C14orf33	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56587400-56599200	Weak transcription	Colonic Mucosa	Colon
2	chr14:56587600-56598000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr14:56591000-56599600	Enhancers	Fetal Thymus	thymus
4	chr14:56591600-56598200	Weak transcription	Fetal Kidney	kidney
5	chr14:56592000-56597800	Weak transcription	Aorta	Aorta
6	chr14:56592000-56598800	Weak transcription	NHLF	lung
7	chr14:56592000-56601800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:56592400-56599800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:56592400-56600400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr14:56593200-56612800	Weak transcription	Brain Angular Gyrus	brain
11	chr14:56593600-56598200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:56593800-56598000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr14:56594200-56598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr14:56594200-56598400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr14:56594200-56599400	Enhancers	Brain Germinal Matrix	brain
16	chr14:56594400-56597800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:56594400-56597800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr14:56594400-56598000	Weak transcription	Primary T cells from cord blood	blood
19	chr14:56594600-56600600	Enhancers	Stomach Mucosa	stomach
20	chr14:56594600-56601400	Enhancers	Colon Smooth Muscle	Colon
21	chr14:56594800-56597400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr14:56595000-56599400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr14:56595000-56599800	Enhancers	Duodenum Mucosa	Duodenum
24	chr14:56595200-56599600	Enhancers	Ovary	ovary
25	chr14:56595600-56597400	Enhancers	Brain Hippocampus Middle	brain
26	chr14:56595600-56598000	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr14:56595600-56607000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr14:56595800-56599600	Enhancers	Primary hematopoietic stem cells	blood
29	chr14:56595800-56600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:56596000-56597400	Enhancers	Adipose Nuclei	Adipose
31	chr14:56596000-56598400	Enhancers	Liver	Liver
32	chr14:56596000-56599000	Enhancers	Brain Anterior Caudate	brain
33	chr14:56596200-56598600	Enhancers	Psoas Muscle	Psoas
34	chr14:56596200-56599200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr14:56596400-56599400	Enhancers	Brain Substantia Nigra	brain
36	chr14:56596600-56597800	Weak transcription	Fetal Brain Female	brain
37	chr14:56596600-56598000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr14:56596600-56598200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr14:56596600-56598400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr14:56596600-56598400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr14:56596600-56599000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr14:56596600-56600200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr14:56596600-56600200	Weak transcription	Esophagus	oesophagus
44	chr14:56596600-56600200	Weak transcription	Right Atrium	heart
45	chr14:56596600-56603600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr14:56596600-56615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr14:56596800-56597600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr14:56596800-56597800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr14:56596800-56598800	Weak transcription	Left Ventricle	heart
50	chr14:56596800-56603600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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