Variant report

Variant	rs6490299
Chromosome Location	chr12:121079798-121079799
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	REST	chr12:121078963-121079808	A549	lung:	n/a	chr12:121079331-121079351 chr12:121079319-121079333 chr12:121079331-121079340 chr12:121079334-121079347
2	REST	chr12:121078925-121079833	PANC-1	pancreas:	n/a	chr12:121079331-121079351 chr12:121079319-121079333 chr12:121079331-121079340 chr12:121079334-121079347
3	MXI1	chr12:121078791-121080242	IMR90	lung:	n/a	n/a
4	REST	chr12:121078980-121079885	PANC-1	pancreas:	n/a	chr12:121079331-121079351 chr12:121079319-121079333 chr12:121079331-121079340 chr12:121079334-121079347
5	REST	chr12:121078611-121080060	HL-60	blood:	n/a	chr12:121079331-121079351 chr12:121079319-121079333 chr12:121079331-121079340 chr12:121079334-121079347
6	REST	chr12:121078204-121079915	ECC-1	luminal epithelium:	n/a	chr12:121079331-121079351 chr12:121079319-121079333 chr12:121079331-121079340 chr12:121079334-121079347
7	REST	chr12:121078802-121080136	A549	lung:	n/a	chr12:121079331-121079351 chr12:121079319-121079333 chr12:121079331-121079340 chr12:121079334-121079347
8	MAZ	chr12:121078810-121079901	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121079422..121081795-chr12:121123452..121125131,2	K562	blood:
2	chr12:120729224..120730765-chr12:121078974..121080739,2	K562	blood:

Variant related genes	Relation type
ENSG00000256008	TF binding region
ENSG00000110917	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12300860	0.89[ASN][1000 genomes]
rs4766972	0.89[ASN][1000 genomes]
rs4766976	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767922	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767923	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57716335	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66473965	0.90[ASN][1000 genomes]
rs7976660	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv3346909	chr12:121077394-121079942	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3334570	chr12:121077719-121079967	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121078000-121079800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:121078200-121079800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:121078800-121079800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:121078800-121079800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
5	chr12:121079000-121080000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:121079000-121080400	Bivalent Enhancer	Fetal Brain Male	brain
7	chr12:121079200-121079800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:121079200-121079800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:121079200-121079800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
10	chr12:121079200-121079800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:121079200-121079800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
12	chr12:121079200-121079800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
13	chr12:121079200-121079800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr12:121079200-121079800	Bivalent Enhancer	Fetal Thymus	thymus
15	chr12:121079200-121080000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr12:121079200-121080000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr12:121079200-121080000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
18	chr12:121079400-121079800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
20	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:121079400-121079800	Bivalent Enhancer	Primary B cells from cord blood	blood
24	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
26	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
27	chr12:121079400-121079800	Bivalent Enhancer	Fetal Kidney	kidney
28	chr12:121079400-121079800	Bivalent Enhancer	Fetal Lung	lung
29	chr12:121079400-121079800	Enhancers	Left Ventricle	heart
30	chr12:121079400-121079800	Enhancers	Pancreas	Pancrea
31	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
32	chr12:121079400-121079800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
33	chr12:121079400-121079800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
34	chr12:121079400-121079800	Enhancers	Spleen	Spleen
35	chr12:121079400-121080000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr12:121079400-121080000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr12:121079400-121080400	Bivalent Enhancer	Esophagus	oesophagus
38	chr12:121079400-121081200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:121079600-121079800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
40	chr12:121079600-121079800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
41	chr12:121079600-121079800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr12:121079600-121079800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:121079600-121079800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:121079600-121079800	Bivalent Enhancer	Primary T cells from cord blood	blood
45	chr12:121079600-121079800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:121079600-121079800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
47	chr12:121079600-121079800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:121079600-121079800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr12:121079600-121079800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr12:121079600-121079800	Bivalent Enhancer	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links