Variant report

Variant	rs4706757
Chromosome Location	chr6:79939847-79939848
allele	A/G
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	CEBPB	chr6:79939792-79940337	MCF-7	breast:	n/a	chr6:79940074-79940085
2	CEBPB	chr6:79939762-79940349	ECC-1	luminal epithelium:	n/a	chr6:79940074-79940085
3	CEBPB	chr6:79939729-79940277	Hela-S3	cervix:	n/a	chr6:79940074-79940085
4	CEBPB	chr6:79939847-79940258	HCT-116	colon:	n/a	chr6:79940074-79940085
5	CEBPB	chr6:79939752-79940282	K562	blood:	n/a	chr6:79940074-79940085
6	CEBPB	chr6:79939620-79940452	MCF-7	breast:	n/a	chr6:79940074-79940085
7	EP300	chr6:79939782-79940253	ECC-1	luminal epithelium:	n/a	n/a
8	CEBPB	chr6:79939691-79940407	A549	lung:	n/a	chr6:79940074-79940085
9	CEBPB	chr6:79939782-79940314	ECC-1	luminal epithelium:	n/a	chr6:79940074-79940085
10	CEBPB	chr6:79939825-79940269	IMR90	lung:	n/a	chr6:79940074-79940085

No.	Distal block	Cell Line	Cell type
1	chr6:79938105..79940918-chr6:79942151..79944715,2	K562	blood:
2	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
3	chr6:79786645..79789143-chr6:79938512..79942027,3	MCF-7	breast:
4	chr6:79934006..79937126-chr6:79938281..79940748,3	K562	blood:

Variant related genes	Relation type
HMGN3-AS1	TF binding region
ENSG00000146247	Chromatin interaction
ENSG00000118418	Chromatin interaction
ENSG00000270362	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10806164	0.93[EUR][1000 genomes]
rs11752249	0.99[EUR][1000 genomes]
rs12191359	0.93[EUR][1000 genomes]
rs12211094	0.93[EUR][1000 genomes]
rs2050436	0.93[EUR][1000 genomes]
rs28360567	0.93[EUR][1000 genomes]
rs28360568	0.93[EUR][1000 genomes]
rs34043789	0.96[EUR][1000 genomes]
rs35711640	0.93[EUR][1000 genomes]
rs4706085	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66732383	0.93[EUR][1000 genomes]
rs6930131	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7750289	0.93[EUR][1000 genomes]
rs7766859	0.93[EUR][1000 genomes]
rs9294132	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9294133	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9294134	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9343882	0.93[EUR][1000 genomes]
rs9361502	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9448657	0.96[EUR][1000 genomes]
rs989191	0.99[EUR][1000 genomes]

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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4706757	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79907400-79942800	Weak transcription	HSMM	muscle
2	chr6:79907600-79940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:79912400-79940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:79917800-79941000	Weak transcription	Hela-S3	cervix
9	chr6:79918200-79942000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:79920400-79940600	Weak transcription	Dnd41	blood
11	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:79925400-79940000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:79925400-79940600	Weak transcription	Placenta	Placenta
14	chr6:79925400-79942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:79925800-79940600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:79925800-79941800	Weak transcription	Brain Angular Gyrus	brain
17	chr6:79925800-79942000	Weak transcription	Adipose Nuclei	Adipose
18	chr6:79925800-79942000	Weak transcription	Brain Anterior Caudate	brain
19	chr6:79925800-79942800	Weak transcription	Liver	Liver
20	chr6:79926600-79942000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:79927400-79942600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:79927600-79940800	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:79927800-79940800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:79927800-79942000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:79927800-79942800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:79927800-79942800	Weak transcription	Primary T cells from cord blood	blood
27	chr6:79928000-79942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:79929000-79942000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:79929000-79942000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:79929200-79941600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:79929600-79941400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:79929800-79941000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:79930200-79941800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:79931200-79942800	Weak transcription	Left Ventricle	heart
35	chr6:79931600-79940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:79931600-79942000	Weak transcription	Gastric	stomach
37	chr6:79932400-79942400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:79933800-79942600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:79934200-79942200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:79934200-79942400	Weak transcription	Primary B cells from cord blood	blood
41	chr6:79934600-79940600	Weak transcription	Fetal Lung	lung
42	chr6:79934600-79941600	Weak transcription	Fetal Intestine Small	intestine
43	chr6:79935800-79941600	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:79935800-79942000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:79936000-79942000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:79936200-79940800	Weak transcription	Right Ventricle	heart
47	chr6:79936200-79941400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:79936200-79941600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:79936200-79942200	Weak transcription	Small Intestine	intestine
50	chr6:79936200-79943000	Weak transcription	Fetal Intestine Large	intestine

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