Variant report

Variant	rs17454108
Chromosome Location	chr2:179987043-179987044
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179983325..179985286-chr2:179986584..179988899,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1048026	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10497534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11892241	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11900884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12105478	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs16866665	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16866673	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs17453976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454192	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454458	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1838872	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2008215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4101465	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4499457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58582728	1.00[AFR][1000 genomes]
rs60072979	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61179885	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433759	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433766	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs879539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
4	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:179972600-180001800	Weak transcription	NHEK	skin
10	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
14	chr2:179973200-179987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:179973200-179988400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:179973200-179988800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:179973200-179989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:179973200-179989400	Weak transcription	Primary T cells from cord blood	blood
19	chr2:179973400-179990000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
21	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
22	chr2:179973400-180012600	Weak transcription	NHLF	lung
23	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:179974400-179994200	Strong transcription	HepG2	liver
25	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
27	chr2:179976600-179989800	Weak transcription	Gastric	stomach
28	chr2:179977200-179988000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:179977400-179987400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:179977400-179987800	Weak transcription	Brain Angular Gyrus	brain
31	chr2:179977400-179988400	Weak transcription	Brain Substantia Nigra	brain
32	chr2:179977400-180004400	Weak transcription	Lung	lung
33	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
34	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
35	chr2:179977600-179988600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:179977800-179988600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
40	chr2:179979400-179988600	Strong transcription	Fetal Muscle Leg	muscle
41	chr2:179980000-180038800	Weak transcription	HMEC	breast
42	chr2:179980000-180056800	Weak transcription	HSMM	muscle
43	chr2:179980400-179989400	Weak transcription	Thymus	Thymus
44	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:179980800-179989400	Weak transcription	Fetal Thymus	thymus
47	chr2:179981000-179991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:179981200-179990200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:179981400-180001800	Weak transcription	Placenta	Placenta
50	chr2:179981400-180005000	Weak transcription	Ovary	ovary

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