Variant report

Variant	rs10789454
Chromosome Location	chr1:45515883-45515884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45503364..45509535-chr1:45510898..45517046,6	K562	blood:
2	chr1:45492852..45494427-chr1:45515259..45518004,2	K562	blood:
3	chr1:45477633..45480305-chr1:45514821..45518438,3	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11211074	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1144868	0.89[EUR][1000 genomes]
rs1226914	0.84[EUR][1000 genomes]
rs1938300	0.85[EUR][1000 genomes]
rs1938301	0.85[EUR][1000 genomes]
rs1938304	0.83[EUR][1000 genomes]
rs2105458	0.85[EUR][1000 genomes]
rs2356302	0.85[EUR][1000 genomes]
rs238249	0.90[EUR][1000 genomes]
rs2997465	0.85[EUR][1000 genomes]
rs3009968	0.85[EUR][1000 genomes]
rs3009969	0.85[EUR][1000 genomes]
rs3009974	0.85[EUR][1000 genomes]
rs346687	0.90[EUR][1000 genomes]
rs346696	0.89[EUR][1000 genomes]
rs346701	0.88[EUR][1000 genomes]
rs346723	0.89[EUR][1000 genomes]
rs346731	0.84[EUR][1000 genomes]
rs346733	0.90[EUR][1000 genomes]
rs346736	0.90[EUR][1000 genomes]
rs346737	0.90[EUR][1000 genomes]
rs3850855	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs415536	0.90[EUR][1000 genomes]
rs4454584	0.84[EUR][1000 genomes]
rs6429557	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
3	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
5	chr1:45497400-45525400	Weak transcription	Gastric	stomach
6	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
7	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
10	chr1:45501800-45516200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
13	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
15	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
16	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:45504800-45516400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
19	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
20	chr1:45508800-45516200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:45509000-45523000	Weak transcription	Brain Angular Gyrus	brain
22	chr1:45509000-45523800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:45509200-45521000	Weak transcription	Brain Anterior Caudate	brain
25	chr1:45509200-45522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:45509600-45516200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:45509600-45516400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:45509600-45522400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:45510000-45516000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:45511200-45521400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:45511400-45521400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:45512400-45523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:45513200-45517400	Strong transcription	Fetal Brain Female	brain
35	chr1:45513600-45516400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:45513600-45519600	Weak transcription	Ovary	ovary
37	chr1:45513600-45525400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:45513600-45526200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:45514400-45519200	Strong transcription	HepG2	liver
40	chr1:45514800-45517200	Strong transcription	Brain Germinal Matrix	brain
41	chr1:45515400-45516600	Enhancers	Primary T cells from cord blood	blood
42	chr1:45515600-45516400	Weak transcription	Fetal Intestine Small	intestine
43	chr1:45515600-45517000	Weak transcription	Brain Substantia Nigra	brain
44	chr1:45515800-45516600	Enhancers	Primary T cells fromperipheralblood	blood

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