Variant report

Variant	rs17397799
Chromosome Location	chr1:45523572-45523573
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45521218..45524154-chr1:45525277..45526789,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1502340	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17394390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938299	1.00[AFR][1000 genomes]
rs2096435	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4660298	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4660837	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788378	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61788379	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61788380	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61788382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788383	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788386	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61788387	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788388	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788389	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788390	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788393	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788427	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61788428	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61788429	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788430	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788436	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788438	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788439	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788440	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788441	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788447	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788449	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788455	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789766	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789768	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789773	0.80[AMR][1000 genomes]
rs61789774	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789775	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789777	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789778	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789782	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789785	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789788	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61789789	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61789808	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61789809	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61789814	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61789816	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61789817	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61789818	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61789819	1.00[AFR][1000 genomes]
rs61789822	1.00[AFR][1000 genomes]
rs61789826	1.00[AFR][1000 genomes]
rs61789830	1.00[AFR][1000 genomes]
rs61789957	1.00[AFR][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:43 , 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	chr1:45497400-45525400	Weak transcription	Gastric	stomach
5	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
6	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
7	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
9	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
11	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
12	chr1:45509000-45523800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:45512400-45523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:45513600-45525400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:45513600-45526200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:45517000-45525600	Weak transcription	Small Intestine	intestine
19	chr1:45517400-45526200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:45517600-45526800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:45517800-45525600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:45520400-45529200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:45521200-45525800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:45521200-45525800	Strong transcription	HepG2	liver
25	chr1:45521200-45526600	Strong transcription	Ovary	ovary
26	chr1:45521400-45525800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:45521400-45526000	Strong transcription	Brain Germinal Matrix	brain
28	chr1:45521400-45527400	Weak transcription	Fetal Intestine Small	intestine
29	chr1:45522200-45524800	Strong transcription	Brain Anterior Caudate	brain
30	chr1:45522400-45524800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr1:45522600-45524600	Strong transcription	Brain Substantia Nigra	brain
32	chr1:45522600-45524600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:45522600-45525800	Strong transcription	Brain Hippocampus Middle	brain
34	chr1:45522600-45526000	Strong transcription	Fetal Brain Female	brain
35	chr1:45522800-45524400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:45523000-45523600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:45523000-45523600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:45523000-45524600	Strong transcription	Aorta	Aorta
39	chr1:45523000-45525200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:45523000-45525200	Strong transcription	Brain Angular Gyrus	brain
41	chr1:45523000-45525400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:45523400-45523600	Strong transcription	Fetal Intestine Large	intestine
43	chr1:45523400-45527400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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