Variant report

Variant	rs7145330
Chromosome Location	chr14:56616639-56616640
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10134875	0.83[EUR][1000 genomes]
rs10150333	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]
rs10782430	0.83[TSI][hapmap]
rs11158077	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs11158082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11158086	0.81[TSI][hapmap]
rs1117310	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11623431	0.81[TSI][hapmap]
rs11627862	0.83[TSI][hapmap]
rs11845193	0.81[TSI][hapmap]
rs11847205	0.83[TSI][hapmap]
rs12432184	0.83[TSI][hapmap]
rs12877991	0.83[TSI][hapmap]
rs12893611	0.83[TSI][hapmap]
rs12897424	0.83[TSI][hapmap]
rs1382973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1479744	0.83[TSI][hapmap]
rs1479745	0.83[TSI][hapmap]
rs1479746	0.80[TSI][hapmap]
rs1479748	0.83[TSI][hapmap]
rs17254064	0.83[TSI][hapmap]
rs173352	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1953211	0.83[TSI][hapmap]
rs2054491	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2054492	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2086326	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2343377	0.80[EUR][1000 genomes]
rs242412	0.89[TSI][hapmap]
rs242420	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs242421	0.81[TSI][hapmap]
rs242578	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3783665	0.83[TSI][hapmap]
rs3783675	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3844020	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3895330	0.83[TSI][hapmap]
rs3912199	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs3912200	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs3912201	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4143949	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4898882	0.81[TSI][hapmap]
rs4898890	0.83[TSI][hapmap]
rs4898891	0.83[TSI][hapmap]
rs4898892	0.83[TSI][hapmap]
rs4901638	0.82[EUR][1000 genomes]
rs4901659	0.81[TSI][hapmap]
rs7140444	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7140575	0.80[EUR][1000 genomes]
rs7142227	0.83[TSI][hapmap]
rs7151741	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7153877	0.80[EUR][1000 genomes]
rs715756	0.81[TSI][hapmap]
rs7160779	0.80[EUR][1000 genomes]
rs8014536	0.83[TSI][hapmap]
rs8016951	0.83[TSI][hapmap]
rs899604	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9646155	0.83[TSI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7145330	CDKN3	cis	parietal	SCAN
rs7145330	GNG11	trans	lymphoblastoid	seeQTL
rs7145330	C14orf33	cis	cerebellum	SCAN
rs7145330	GNPNAT1	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56611400-56620000	Enhancers	Colon Smooth Muscle	Colon
2	chr14:56612200-56617000	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr14:56612200-56618000	Enhancers	Rectal Smooth Muscle	rectum
4	chr14:56612800-56617600	Enhancers	Brain Angular Gyrus	brain
5	chr14:56613200-56620000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:56613400-56620000	Weak transcription	HUVEC	blood vessel
7	chr14:56613600-56617800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr14:56613600-56619800	Enhancers	Fetal Brain Male	brain
9	chr14:56613800-56618200	Enhancers	Primary hematopoietic stem cells	blood
10	chr14:56613800-56619400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr14:56614000-56617000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr14:56614200-56618800	Enhancers	Primary T cells from cord blood	blood
13	chr14:56614400-56617000	Enhancers	Primary B cells from cord blood	blood
14	chr14:56614600-56617000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr14:56614600-56617200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:56614600-56617800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr14:56614600-56618400	Flanking Active TSS	Dnd41	blood
18	chr14:56614600-56619000	Enhancers	Fetal Thymus	thymus
19	chr14:56614800-56616800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr14:56614800-56618000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr14:56614800-56618000	Enhancers	Brain Germinal Matrix	brain
22	chr14:56614800-56618400	Enhancers	Thymus	Thymus
23	chr14:56615000-56617800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr14:56615000-56620000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr14:56615200-56617200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:56615400-56617000	Enhancers	Stomach Smooth Muscle	stomach
27	chr14:56615400-56617600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr14:56615400-56618600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr14:56615400-56618800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:56615400-56626800	Weak transcription	Left Ventricle	heart
31	chr14:56615600-56616800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr14:56615600-56617400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr14:56615600-56617400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr14:56615600-56617400	Weak transcription	Gastric	stomach
35	chr14:56615600-56617800	Weak transcription	Esophagus	oesophagus
36	chr14:56615600-56621000	Weak transcription	Small Intestine	intestine
37	chr14:56615600-56639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr14:56615800-56616800	Weak transcription	Brain Anterior Caudate	brain
39	chr14:56615800-56616800	Weak transcription	Pancreas	Pancrea
40	chr14:56615800-56617400	Weak transcription	Ovary	ovary
41	chr14:56615800-56618800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr14:56615800-56619000	Weak transcription	Brain Substantia Nigra	brain
43	chr14:56615800-56623200	Weak transcription	Spleen	Spleen
44	chr14:56615800-56625800	Weak transcription	Lung	lung
45	chr14:56615800-56626800	Weak transcription	Stomach Mucosa	stomach
46	chr14:56616000-56617000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr14:56616000-56617000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr14:56616000-56618200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr14:56616000-56625800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr14:56616200-56616800	Weak transcription	Brain Hippocampus Middle	brain

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