Variant report

Variant	rs2343376
Chromosome Location	chr14:56618078-56618079
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56617611..56619995-chr14:56685329..56687097,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10144612	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs10483656	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1427556	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap]
rs17688725	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17688801	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17689278	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17761563	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs17762499	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17762733	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17832675	0.90[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1951955	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2035283	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28712711	0.83[EUR][1000 genomes]
rs2880615	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3850298	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3912203	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4127813	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8020301	0.81[CEU][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
rs2343376	PSMC6	cis	cerebellum	SCAN
rs2343376	ERO1L	cis	parietal	SCAN
rs2343376	ARID4A	cis	cerebellum	SCAN
rs2343376	MAPK1IP1L	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56611400-56620000	Enhancers	Colon Smooth Muscle	Colon
2	chr14:56613200-56620000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:56613400-56620000	Weak transcription	HUVEC	blood vessel
4	chr14:56613600-56619800	Enhancers	Fetal Brain Male	brain
5	chr14:56613800-56618200	Enhancers	Primary hematopoietic stem cells	blood
6	chr14:56613800-56619400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr14:56614200-56618800	Enhancers	Primary T cells from cord blood	blood
8	chr14:56614600-56618400	Flanking Active TSS	Dnd41	blood
9	chr14:56614600-56619000	Enhancers	Fetal Thymus	thymus
10	chr14:56614800-56618400	Enhancers	Thymus	Thymus
11	chr14:56615000-56620000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr14:56615400-56618600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:56615400-56618800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:56615400-56626800	Weak transcription	Left Ventricle	heart
15	chr14:56615600-56621000	Weak transcription	Small Intestine	intestine
16	chr14:56615600-56639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:56615800-56618800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr14:56615800-56619000	Weak transcription	Brain Substantia Nigra	brain
19	chr14:56615800-56623200	Weak transcription	Spleen	Spleen
20	chr14:56615800-56625800	Weak transcription	Lung	lung
21	chr14:56615800-56626800	Weak transcription	Stomach Mucosa	stomach
22	chr14:56616000-56618200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr14:56616000-56625800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr14:56616200-56619000	Weak transcription	Fetal Intestine Small	intestine
25	chr14:56616200-56621000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr14:56616200-56621200	Weak transcription	Aorta	Aorta
27	chr14:56616200-56626000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr14:56616800-56619000	Enhancers	Pancreas	Pancrea
29	chr14:56616800-56640200	Weak transcription	Fetal Stomach	stomach
30	chr14:56617000-56618800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr14:56617000-56618800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr14:56617200-56620200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr14:56617200-56627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr14:56617400-56618200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:56617400-56618400	Enhancers	Ovary	ovary
36	chr14:56617600-56618600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr14:56617600-56619800	Enhancers	Fetal Brain Female	brain
38	chr14:56617600-56623000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr14:56617800-56618400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr14:56617800-56618400	Enhancers	GM12878-XiMat	blood
41	chr14:56617800-56618800	Enhancers	Esophagus	oesophagus
42	chr14:56617800-56619800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr14:56617800-56620400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr14:56617800-56623000	Weak transcription	Fetal Lung	lung
45	chr14:56618000-56618200	Enhancers	Gastric	stomach
46	chr14:56618000-56620400	Weak transcription	Brain Germinal Matrix	brain
47	chr14:56618000-56629200	Weak transcription	Rectal Smooth Muscle	rectum

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