Variant report

Variant	rs17466896
Chromosome Location	chr1:222883815-222883816
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	CUX1	chr1:222882938-222883943	K562	blood:	n/a	n/a
2	NR2F2	chr1:222882792-222883970	K562	blood:	n/a	n/a
3	RCOR1	chr1:222882969-222883854	K562	blood:	n/a	n/a
4	TEAD4	chr1:222882801-222883853	K562	blood:	n/a	n/a
5	MAFF	chr1:222882950-222883857	K562	blood:	n/a	n/a
6	GATA1	chr1:222882747-222884443	K562	blood:	n/a	chr1:222883269-222883277 chr1:222883982-222883991 chr1:222883978-222883994
7	POLR2A	chr1:222883771-222884018	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222762075..222764721-chr1:222883311..222887470,5	K562	blood:
2	chr1:222815622..222820703-chr1:222883498..222888165,14	K562	blood:

Variant related genes	Relation type
RN7SL276P	TF binding region
BROX	TF binding region
ENSG00000143498	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000225265	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10495200	0.96[EUR][1000 genomes]
rs11118971	1.00[ASN][1000 genomes]
rs12058171	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163431	1.00[ASN][1000 genomes]
rs17163437	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163441	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474333	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17531063	0.84[AFR][1000 genomes]
rs17531468	0.84[AFR][1000 genomes]
rs17532610	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35684750	0.81[EUR][1000 genomes]
rs35762933	0.82[EUR][1000 genomes]
rs3748629	0.84[AFR][1000 genomes]
rs3748631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41424447	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124884	0.81[EUR][1000 genomes]
rs7520650	0.81[EUR][1000 genomes]
rs9286760	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441846	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441936	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
4	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
5	chr1:222845000-222884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:222855200-222884600	Weak transcription	Pancreas	Pancrea
7	chr1:222860000-222884600	Weak transcription	Left Ventricle	heart
8	chr1:222860200-222884000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:222860200-222884200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:222860200-222884400	Weak transcription	Placenta	Placenta
11	chr1:222860200-222884600	Weak transcription	Aorta	Aorta
12	chr1:222860200-222884600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:222860200-222884600	Weak transcription	Gastric	stomach
14	chr1:222860200-222884600	Weak transcription	Lung	lung
15	chr1:222860600-222884200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:222861000-222885000	Weak transcription	Spleen	Spleen
17	chr1:222873800-222884600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:222874000-222884600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:222876200-222884000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:222876200-222884200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:222876200-222884400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:222876400-222884000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:222877600-222884000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:222880600-222884000	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr1:222881800-222884600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:222882000-222884000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:222882000-222884400	Enhancers	Colon Smooth Muscle	Colon
28	chr1:222882000-222884600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:222882200-222884600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:222882400-222884000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:222882400-222884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:222882400-222884600	Enhancers	Small Intestine	intestine
33	chr1:222882800-222884000	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:222882800-222884000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:222882800-222884600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:222883000-222884000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:222883000-222884000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:222883000-222884000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:222883000-222884200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:222883000-222884200	Enhancers	Primary T cells from cord blood	blood
41	chr1:222883000-222884200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:222883000-222884200	Enhancers	Adipose Nuclei	Adipose
43	chr1:222883000-222884200	Flanking Active TSS	K562	blood
44	chr1:222883000-222884600	Enhancers	Brain Cingulate Gyrus	brain
45	chr1:222883200-222884000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:222883200-222884000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr1:222883200-222884000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:222883200-222884000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:222883200-222884000	Enhancers	Fetal Heart	heart
50	chr1:222883200-222884000	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links