Variant report

Variant	rs60502055
Chromosome Location	chr9:95076120-95076121
allele	A/C
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	chr9:95076090-95076128	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr9:95075981-95076132	GM12878	blood:	n/a	n/a
3	POLR2A	chr9:95076001-95076125	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:95075966-95076531	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95055364..95058067-chr9:95075208..95077648,2	MCF-7	breast:
2	chr9:95075884..95078062-chr9:95079368..95081313,2	MCF-7	breast:

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

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs15717	1.00[AFR][1000 genomes]
rs16908281	1.00[AFR][1000 genomes]
rs16908298	1.00[AFR][1000 genomes];1.00[AMR][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[AFR][1000 genomes]
rs2274967	1.00[AFR][1000 genomes]
rs3737147	0.93[AFR][1000 genomes]
rs3847319	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]
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	0.95[AFR][1000 genomes]
rs7027344	0.83[AFR][1000 genomes]
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	0.93[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	chr9:95062000-95081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:95062200-95085800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr9:95062800-95083600	Strong transcription	Primary B cells from cord blood	blood
25	chr9:95071400-95077200	Weak transcription	Small Intestine	intestine
26	chr9:95072000-95085800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:95072600-95079200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:95072800-95078000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:95073000-95078200	Weak transcription	Fetal Brain Male	brain
30	chr9:95073000-95078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:95073000-95081200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:95073200-95079200	Weak transcription	Esophagus	oesophagus
33	chr9:95073200-95086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr9:95073400-95078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:95073400-95078200	Weak transcription	Spleen	Spleen
36	chr9:95073400-95078800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr9:95073400-95078800	Weak transcription	Right Ventricle	heart
38	chr9:95073400-95079200	Weak transcription	Colon Smooth Muscle	Colon
39	chr9:95073600-95076600	Weak transcription	Osteobl	bone
40	chr9:95073600-95077000	Weak transcription	Ovary	ovary
41	chr9:95073600-95077000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:95073600-95077200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:95073600-95077400	Weak transcription	NHDF-Ad	bronchial
44	chr9:95073600-95077800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:95073600-95078200	Weak transcription	Gastric	stomach
46	chr9:95073600-95078400	Weak transcription	Thymus	Thymus
47	chr9:95073600-95078600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr9:95073600-95078800	Weak transcription	Colonic Mucosa	Colon
49	chr9:95073600-95079200	Weak transcription	Pancreas	Pancrea
50	chr9:95073800-95076800	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links