Variant report

Variant	rs11494
Chromosome Location	chr10:45500221-45500222
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	RFX5	chr10:45500209-45500392	HepG2	liver:	n/a	n/a
2	FOXA1	chr10:45500093-45500677	HepG2	liver:	n/a	n/a
3	NR2F2	chr10:45500063-45500599	HepG2	liver:	n/a	n/a
4	POLR2A	chr10:45499672-45503840	K562	blood:	n/a	n/a
5	RXRA	chr10:45500157-45500401	HepG2	liver:	n/a	n/a
6	FOXA2	chr10:45500079-45501363	HepG2	liver:	n/a	chr10:45500780-45500792
7	EP300	chr10:45500075-45500524	HepG2	liver:	n/a	n/a
8	FOXA1	chr10:45500109-45500623	HepG2	liver:	n/a	n/a
9	MAFK	chr10:45500140-45500352	HepG2	liver:	n/a	n/a
10	FOXA1	chr10:45500108-45500519	HepG2	liver:	n/a	n/a
11	ARID3A	chr10:45500124-45501192	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45495742..45497934-chr10:45498787..45500751,2	MCF-7	breast:
2	chr10:45499571..45502259-chr10:45742998..45745677,2	K562	blood:

Variant related genes	Relation type
C10orf25	TF binding region
ENSG00000165512	Chromatin interaction
ENSG00000165511	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10047345	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11239310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239337	0.94[ASW][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12257275	0.89[EUR][1000 genomes]
rs12264627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157327	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095088	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2104898	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4339993	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4573635	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56259997	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57046651	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59085162	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60581169	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61183370	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593454	0.96[EUR][1000 genomes]
rs7080655	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095202	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72782417	0.92[EUR][1000 genomes]
rs73283471	0.92[EUR][1000 genomes]
rs7902918	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915377	0.98[EUR][1000 genomes]
rs7918953	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45497000-45511000	Weak transcription	Gastric	stomach
2	chr10:45497200-45504000	Weak transcription	Esophagus	oesophagus
3	chr10:45497400-45501200	Weak transcription	Aorta	Aorta
4	chr10:45497400-45501400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:45497400-45503800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:45497400-45504000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:45497400-45504000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:45497600-45502800	Weak transcription	Fetal Brain Male	brain
9	chr10:45497600-45503800	Weak transcription	Brain Substantia Nigra	brain
10	chr10:45497600-45504000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:45497800-45500600	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr10:45497800-45500600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr10:45497800-45502200	Weak transcription	Right Ventricle	heart
14	chr10:45497800-45504000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:45498200-45500600	ZNF genes & repeats	GM12878-XiMat	blood
16	chr10:45498200-45503800	Weak transcription	Colon Smooth Muscle	Colon
17	chr10:45498200-45503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:45498200-45504000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:45498400-45500400	Genic enhancers	Primary hematopoietic stem cells	blood
20	chr10:45498400-45500600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
21	chr10:45498400-45501200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr10:45498400-45503800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:45498600-45500400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:45498600-45500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:45498600-45500800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr10:45498600-45501400	Strong transcription	Fetal Lung	lung
27	chr10:45498800-45500400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:45498800-45500400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
29	chr10:45498800-45500400	Strong transcription	Rectal Smooth Muscle	rectum
30	chr10:45498800-45500600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr10:45498800-45500600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr10:45498800-45500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:45498800-45500600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
34	chr10:45498800-45500600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:45498800-45500600	Strong transcription	Brain Hippocampus Middle	brain
36	chr10:45498800-45500800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:45498800-45500800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr10:45498800-45501200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr10:45498800-45501200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:45498800-45501200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr10:45498800-45501200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr10:45498800-45501600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr10:45499000-45500400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr10:45499000-45500400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr10:45499000-45500400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:45499000-45500400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr10:45499000-45500600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:45499000-45500800	Strong transcription	Fetal Kidney	kidney
49	chr10:45499000-45500800	Strong transcription	Left Ventricle	heart
50	chr10:45499000-45501000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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