Variant report

Variant	rs16908298
Chromosome Location	chr9:95081569-95081570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:95081316-95081596	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95051112..95065542-chr9:95079443..95091389,38	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IARS-1	chr9:95081503-95081638	NR_046106

Variant related genes	Relation type
NOL8	TF binding region
ENSG00000239183	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs15717	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16908281	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16908313	1.00[AMR][1000 genomes]
rs1868027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2236343	0.93[AFR][1000 genomes]
rs2236344	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2274967	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3737147	0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs3847319	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs57507064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57537991	1.00[AMR][1000 genomes]
rs57720908	1.00[AMR][1000 genomes]
rs58545014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59083571	0.93[AFR][1000 genomes]
rs59203890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59274719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59491936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59541513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59627747	0.89[AFR][1000 genomes]
rs59633583	0.90[AFR][1000 genomes]
rs60502055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60556849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60752945	0.93[AFR][1000 genomes]
rs60945405	0.95[AFR][1000 genomes]
rs61217521	0.97[AFR][1000 genomes]
rs67546506	0.93[AFR][1000 genomes]
rs7024757	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7027344	0.83[AFR][1000 genomes]
rs7035992	1.00[YRI][hapmap]
rs73516549	0.95[AFR][1000 genomes]
rs73516561	0.95[AFR][1000 genomes]
rs73516586	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73516588	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73516599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73518427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73518450	1.00[AMR][1000 genomes]
rs73518492	1.00[AMR][1000 genomes]
rs73520510	1.00[AMR][1000 genomes]
rs73520539	0.90[AFR][1000 genomes]
rs73520554	0.83[AFR][1000 genomes]
rs7853817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7868362	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7872423	0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs7875329	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95056800-95086800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:95057000-95087000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:95058000-95086200	Weak transcription	Stomach Mucosa	stomach
4	chr9:95058200-95085800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:95058400-95085600	Strong transcription	Placenta	Placenta
6	chr9:95058400-95085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:95058400-95085800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:95058400-95086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:95058600-95085800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:95058600-95085800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:95059200-95085600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr9:95059200-95085600	Strong transcription	Fetal Intestine Large	intestine
13	chr9:95059200-95085800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:95059200-95085800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:95059400-95085600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:95059400-95085600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:95059400-95085800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:95059400-95085800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:95059600-95085600	Strong transcription	Primary T cells from cord blood	blood
20	chr9:95060000-95085600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr9:95060200-95083200	Strong transcription	Fetal Muscle Leg	muscle
22	chr9:95062200-95085800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr9:95062800-95083600	Strong transcription	Primary B cells from cord blood	blood
24	chr9:95072000-95085800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:95073200-95086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr9:95074800-95082000	Weak transcription	Psoas Muscle	Psoas
27	chr9:95075000-95085600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr9:95075200-95085600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:95075400-95082400	Strong transcription	Fetal Lung	lung
30	chr9:95075400-95085600	Strong transcription	Adipose Nuclei	Adipose
31	chr9:95075400-95085600	Strong transcription	Brain Hippocampus Middle	brain
32	chr9:95075400-95085800	Strong transcription	Fetal Thymus	thymus
33	chr9:95075400-95086200	Strong transcription	A549	lung
34	chr9:95075600-95083000	Strong transcription	Fetal Brain Female	brain
35	chr9:95075600-95085800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:95075600-95085800	Strong transcription	NH-A	brain
37	chr9:95075800-95083000	Strong transcription	Brain Germinal Matrix	brain
38	chr9:95075800-95085400	Strong transcription	HepG2	liver
39	chr9:95075800-95085600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:95076000-95083800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr9:95076000-95085600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr9:95076000-95085800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr9:95076000-95085800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr9:95076200-95082800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:95076200-95082800	Strong transcription	Left Ventricle	heart
46	chr9:95076200-95083400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr9:95076200-95085000	Strong transcription	Hela-S3	cervix
48	chr9:95076200-95085800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:95076200-95085800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:95076400-95085600	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links