Variant report

Variant	rs56291725
Chromosome Location	chr10:50289985-50289986
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	MAFK	chr10:50289971-50290318	HepG2	liver:	n/a	n/a
2	CTBP2	chr10:50289439-50290190	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOXA1	chr10:50289808-50290154	HepG2	liver:	n/a	n/a
4	MXI1	chr10:50289968-50290185	H1-hESC	embryonic stem cell:	n/a	n/a
5	BACH1	chr10:50289878-50290189	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOXA1	chr10:50289935-50290185	HepG2	liver:	n/a	n/a
7	SP1	chr10:50289836-50290147	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXA2	chr10:50289914-50290174	HepG2	liver:	n/a	n/a
9	HDAC2	chr10:50289855-50290157	H1-hESC	embryonic stem cell:	n/a	chr10:50289904-50289918
10	YY1	chr10:50289960-50290234	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAFK	chr10:50289974-50290296	HepG2	liver:	n/a	n/a
12	FOXA1	chr10:50289874-50290211	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50288196..50290467-chr10:50297375..50300354,2	K562	blood:

Variant related genes	Relation type
VSTM4	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs12244666	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12244748	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12253426	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12255090	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12256777	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12257242	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261297	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12765281	0.88[EUR][1000 genomes]
rs12769361	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12774293	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12776460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011744	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17011746	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17011757	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17700872	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17701186	0.88[EUR][1000 genomes]
rs17773851	0.88[EUR][1000 genomes]
rs2003044	0.81[EUR][1000 genomes]
rs2137911	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2137912	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2137914	0.94[ASN][1000 genomes]
rs2246673	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246937	0.94[ASN][1000 genomes]
rs2264846	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2264847	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2490838	0.85[EUR][1000 genomes]
rs2725179	0.85[EUR][1000 genomes]
rs2725181	0.84[EUR][1000 genomes]
rs2725184	0.86[EUR][1000 genomes]
rs2725185	0.86[EUR][1000 genomes]
rs2725190	0.85[EUR][1000 genomes]
rs2804937	0.84[EUR][1000 genomes]
rs34062275	0.87[EUR][1000 genomes]
rs34110351	0.88[EUR][1000 genomes]
rs34289781	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34364659	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34467986	0.88[EUR][1000 genomes]
rs34574986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34640094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35341824	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35462783	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35905744	0.88[EUR][1000 genomes]
rs35922675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924984	0.95[ASN][1000 genomes]
rs3924985	0.93[ASN][1000 genomes]
rs4073138	0.86[EUR][1000 genomes]
rs4073139	0.87[EUR][1000 genomes]
rs4364979	0.86[EUR][1000 genomes]
rs4400713	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4402204	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4445564	0.96[EUR][1000 genomes]
rs4468264	0.97[ASN][1000 genomes]
rs4481947	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4497319	0.97[ASN][1000 genomes]
rs4508127	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4550151	0.97[ASN][1000 genomes]
rs4600129	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4644582	0.86[EUR][1000 genomes]
rs55947405	0.86[EUR][1000 genomes]
rs58154726	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58893558	0.86[EUR][1000 genomes]
rs67269950	0.88[EUR][1000 genomes]
rs68065270	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7070387	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7073208	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7081243	0.88[EUR][1000 genomes]
rs7084112	0.99[ASN][1000 genomes]
rs7085823	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088718	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7098134	0.99[ASN][1000 genomes]
rs7100655	0.87[EUR][1000 genomes]
rs72785015	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7896344	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7904272	0.95[ASN][1000 genomes]
rs7907959	0.97[ASN][1000 genomes]
rs9804403	0.93[EUR][1000 genomes];0.95[ASN][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	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50272600-50294200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr10:50283200-50298200	Weak transcription	Spleen	Spleen
3	chr10:50284800-50292400	Enhancers	Liver	Liver
4	chr10:50285200-50292400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr10:50286000-50292400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:50287000-50290200	Enhancers	Fetal Intestine Small	intestine
7	chr10:50287200-50290000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:50287200-50290400	Enhancers	K562	blood
9	chr10:50287200-50292200	Enhancers	Adipose Nuclei	Adipose
10	chr10:50287200-50292400	Enhancers	Brain Substantia Nigra	brain
11	chr10:50287600-50290400	Enhancers	Fetal Intestine Large	intestine
12	chr10:50288000-50291400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr10:50288000-50291400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr10:50288200-50291000	Enhancers	Fetal Muscle Leg	muscle
15	chr10:50288200-50291400	Enhancers	Brain Angular Gyrus	brain
16	chr10:50288200-50292000	Enhancers	Fetal Muscle Trunk	muscle
17	chr10:50288200-50292000	Genic enhancers	Fetal Stomach	stomach
18	chr10:50288200-50292200	Enhancers	Colon Smooth Muscle	Colon
19	chr10:50288200-50292200	Enhancers	Left Ventricle	heart
20	chr10:50288200-50292200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr10:50288200-50293200	Enhancers	Right Ventricle	heart
22	chr10:50288400-50290200	Enhancers	NHLF	lung
23	chr10:50288400-50291000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:50288400-50291400	Enhancers	Brain Cingulate Gyrus	brain
25	chr10:50288400-50291600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr10:50288400-50292400	Enhancers	Brain Hippocampus Middle	brain
27	chr10:50288400-50292600	Enhancers	Brain Anterior Caudate	brain
28	chr10:50288400-50292800	Enhancers	Ovary	ovary
29	chr10:50288400-50293600	Enhancers	HSMMtube	muscle
30	chr10:50288600-50290800	Weak transcription	Brain Germinal Matrix	brain
31	chr10:50288600-50291600	Enhancers	Placenta	Placenta
32	chr10:50288600-50292200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:50288800-50290200	Bivalent Enhancer	Fetal Lung	lung
34	chr10:50289000-50290200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr10:50289000-50291000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:50289000-50291200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr10:50289000-50291400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:50289000-50291400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:50289000-50291800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:50289000-50291800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr10:50289000-50292200	Enhancers	Fetal Brain Male	brain
42	chr10:50289000-50294200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr10:50289200-50291600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr10:50289200-50292200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:50289200-50292200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr10:50289200-50294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:50289400-50290000	Enhancers	H9 Cell Line	embryonic stem cell
48	chr10:50289400-50290000	Bivalent Enhancer	HepG2	liver
49	chr10:50289400-50290200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr10:50289400-50290200	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links