Variant report

Variant	rs11954382
Chromosome Location	chr5:178320846-178320847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178311231..178313312-chr5:178319689..178322645,2	K562	blood:

Variant related genes	Relation type
ENSG00000206624	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10039708	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11948175	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11948664	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11948690	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11949180	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11949181	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11949892	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11949941	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11950641	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11950746	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11952790	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11955047	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11958804	0.88[AMR][1000 genomes]
rs11958887	1.00[CEU][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11958941	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11960942	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12186577	1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12186584	1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12187167	1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12553	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1566106	0.92[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17664194	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs35609799	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35957383	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56814168	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56872885	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56932649	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56951084	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57153194	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57426447	0.96[EUR][1000 genomes]
rs58354049	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58554591	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58672680	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58679434	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58941917	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59242428	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59736551	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59829327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59849584	0.82[EUR][1000 genomes]
rs59994898	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60178472	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60277514	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60417551	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60601817	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60813042	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61295075	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61310482	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61492890	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61744382	0.82[EUR][1000 genomes]
rs62395084	0.84[EUR][1000 genomes]
rs6600991	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6859174	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6861717	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6862829	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6863160	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863202	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863603	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6865216	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6866591	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6870926	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6877663	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6878353	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6882396	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6883566	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6887256	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6890083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6894878	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6895371	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7706558	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7724141	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs7727497	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7729560	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7729717	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7731067	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11954382	ZNF354B	cis	multi-tissue	Pritchard
rs11954382	CNOT6	cis	cerebellum	SCAN
rs11954382	NOP16	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178308400-178322600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178311200-178322400	Weak transcription	Hela-S3	cervix
3	chr5:178313600-178322600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:178313600-178322800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:178314400-178325000	Weak transcription	Fetal Brain Male	brain
6	chr5:178315600-178322400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:178315600-178322600	Weak transcription	Brain Angular Gyrus	brain
8	chr5:178317000-178322600	Weak transcription	Right Ventricle	heart
9	chr5:178317200-178322200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:178317200-178322400	Weak transcription	Brain Anterior Caudate	brain
11	chr5:178317200-178322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:178317200-178322600	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:178317200-178322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:178317200-178322800	Weak transcription	Gastric	stomach
15	chr5:178317400-178321000	Weak transcription	Adipose Nuclei	Adipose
16	chr5:178317400-178322400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:178317400-178322400	Weak transcription	Brain Germinal Matrix	brain
18	chr5:178317400-178322400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:178317400-178322400	Weak transcription	Brain Substantia Nigra	brain
20	chr5:178317400-178322400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:178317400-178322400	Weak transcription	Psoas Muscle	Psoas
22	chr5:178317400-178322400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:178317400-178322400	Weak transcription	Thymus	Thymus
24	chr5:178317400-178322600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:178317400-178322600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:178317400-178322600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:178317400-178322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:178317400-178322600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:178317400-178322600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:178317400-178322600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:178317400-178322600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:178317400-178322600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:178317400-178322600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:178317400-178322600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:178317400-178322600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:178317400-178322600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:178317400-178322600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:178317400-178322600	Weak transcription	Aorta	Aorta
39	chr5:178317400-178322600	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:178317400-178322600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:178317400-178322600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:178317400-178322600	Weak transcription	Fetal Lung	lung
43	chr5:178317400-178322600	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:178317400-178322600	Weak transcription	Fetal Stomach	stomach
45	chr5:178317400-178322600	Weak transcription	Left Ventricle	heart
46	chr5:178317400-178322600	Weak transcription	Pancreas	Pancrea
47	chr5:178317400-178322600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:178317400-178322600	Weak transcription	Spleen	Spleen
49	chr5:178317400-178322600	Weak transcription	HSMMtube	muscle
50	chr5:178317400-178322600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links