Variant report

Variant	rs16888693
Chromosome Location	chr8:117734923-117734924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10505288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11996147	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12541592	0.83[ASN][1000 genomes]
rs12547063	0.85[JPT][hapmap]
rs12548564	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs12548586	0.84[ASN][1000 genomes]
rs1343663	0.83[ASN][1000 genomes]
rs16888632	0.81[ASN][1000 genomes]
rs16888671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16888728	1.00[ASW][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap]
rs1867840	0.88[ASW][hapmap];0.90[YRI][hapmap]
rs28649280	0.82[AFR][1000 genomes]
rs28651059	0.93[AFR][1000 genomes]
rs4289842	0.81[AFR][1000 genomes]
rs56316062	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836328	0.88[AFR][1000 genomes]
rs66883336	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6983626	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs7014328	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs7014359	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs7388498	0.96[YRI][hapmap]
rs764938	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs7823271	0.93[AFR][1000 genomes]
rs7825662	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7828067	0.88[ASW][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs7832540	0.94[AFR][1000 genomes]
rs7833306	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7837208	0.88[ASW][hapmap];0.93[YRI][hapmap]
rs979867	0.82[ASW][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap]

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	nsv530386	chr8:117509968-118391406	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16888693	C8orf53	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:117722000-117735600	Weak transcription	Brain Hippocampus Middle	brain
2	chr8:117722000-117740800	Weak transcription	NHLF	lung
3	chr8:117722400-117738800	Weak transcription	Small Intestine	intestine
4	chr8:117722600-117740800	Weak transcription	HSMMtube	muscle
5	chr8:117724600-117738800	Weak transcription	Psoas Muscle	Psoas
6	chr8:117726800-117735800	Weak transcription	HSMM	muscle
7	chr8:117728000-117740800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:117728000-117740800	Weak transcription	Osteobl	bone
9	chr8:117728600-117740400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:117728800-117739400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:117729000-117736000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:117730400-117735000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:117730800-117736800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr8:117731200-117736600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr8:117731200-117739400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:117731400-117737600	Weak transcription	Fetal Brain Male	brain
17	chr8:117731400-117739400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr8:117731400-117740200	ZNF genes & repeats	GM12878-XiMat	blood
19	chr8:117732000-117736400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr8:117732200-117735400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:117732600-117735000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
22	chr8:117732600-117735000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:117732600-117735000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
24	chr8:117732600-117735000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr8:117732600-117735400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
26	chr8:117732600-117735600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr8:117732600-117735800	ZNF genes & repeats	K562	blood
28	chr8:117732600-117736200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr8:117732600-117736600	ZNF genes & repeats	Dnd41	blood
30	chr8:117732600-117738200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr8:117732800-117735000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
32	chr8:117732800-117738400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr8:117733000-117735000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:117733000-117735000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr8:117733000-117736400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:117733000-117739800	Weak transcription	Fetal Heart	heart
37	chr8:117733000-117740800	Weak transcription	NHDF-Ad	bronchial
38	chr8:117733000-117742400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr8:117733600-117737000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr8:117733600-117737000	Strong transcription	Hela-S3	cervix
41	chr8:117733600-117737400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr8:117733600-117738400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr8:117733600-117740800	Weak transcription	Aorta	Aorta
44	chr8:117733600-117740800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr8:117733600-117741000	Weak transcription	HUVEC	blood vessel
46	chr8:117733600-117742400	Weak transcription	Right Ventricle	heart
47	chr8:117733600-117745000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr8:117733600-117745200	Weak transcription	Brain Anterior Caudate	brain
49	chr8:117733600-117766600	Weak transcription	Fetal Lung	lung
50	chr8:117733600-117766800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links