Variant report

Variant	rs56287743
Chromosome Location	chr1:160096358-160096359
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	CEBPB	chr1:160096256-160096413	K562	blood:	n/a	chr1:160096315-160096326
2	CEBPB	chr1:160096210-160096438	HepG2	liver:	n/a	chr1:160096315-160096326
3	RCOR1	chr1:160096268-160096427	K562	blood:	n/a	n/a

Variant related genes	Relation type
ATP1A2	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11265328	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12402134	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12407381	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12408200	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12410866	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17846705	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17846715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17846717	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17846718	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3761684	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41288127	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55845795	0.83[ASN][1000 genomes]
rs55884181	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56003400	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv872490	chr1:160083012-160121488	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160088000-160097200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:160088000-160146200	Weak transcription	Spleen	Spleen
3	chr1:160088800-160107400	Weak transcription	Fetal Brain Female	brain
4	chr1:160089000-160097400	Weak transcription	Ovary	ovary
5	chr1:160090200-160104600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:160090600-160112600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:160092000-160097200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:160092400-160112200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:160092800-160100800	Strong transcription	Fetal Stomach	stomach
10	chr1:160093000-160096400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:160093000-160098600	Enhancers	Placenta	Placenta
12	chr1:160093400-160098000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:160093600-160099800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:160093800-160096800	Weak transcription	Brain Substantia Nigra	brain
15	chr1:160093800-160098400	Enhancers	HepG2	liver
16	chr1:160093800-160101200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:160093800-160101800	Weak transcription	Gastric	stomach
18	chr1:160093800-160106600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:160094000-160096400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:160094000-160096400	Enhancers	Osteobl	bone
21	chr1:160094000-160097400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:160094000-160112000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:160094200-160096400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:160094200-160096400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:160094400-160096600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:160094400-160097200	Weak transcription	Pancreas	Pancrea
27	chr1:160094600-160097200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:160094600-160100800	Enhancers	HSMM	muscle
29	chr1:160094800-160097200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:160094800-160097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:160094800-160097400	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:160094800-160110200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:160095000-160097200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:160095000-160097200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:160095000-160097200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:160095000-160097200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:160095000-160097400	Strong transcription	Colon Smooth Muscle	Colon
38	chr1:160095000-160099400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:160095000-160103200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:160095200-160096400	Enhancers	A549	lung
41	chr1:160095200-160097200	Weak transcription	Lung	lung
42	chr1:160095200-160097200	Weak transcription	Right Ventricle	heart
43	chr1:160095200-160097200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:160095200-160097400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:160095200-160097600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:160095400-160098600	Weak transcription	Fetal Heart	heart
47	chr1:160095400-160108200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:160095600-160096400	Enhancers	HSMMtube	muscle
49	chr1:160095600-160097600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:160095800-160097000	Genic enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links