Variant report

Variant	rs4148050
Chromosome Location	chr1:94933958-94933959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94923038..94925155-chr1:94932732..94934568,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10157506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1034363	0.88[EUR][1000 genomes]
rs1041282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165149	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11576665	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11581292	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11582033	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1158254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585880	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12120731	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127355	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130330	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12131298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12143221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12143512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16946	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17410399	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1983859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2147794	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2794470	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4148042	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4148052	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4148060	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4536006	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847303	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55801886	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56353982	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61772847	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61772851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61772854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs698950	0.83[EUR][1000 genomes]
rs7555399	0.90[EUR][1000 genomes]
rs841692	0.88[EUR][1000 genomes]
rs841695	0.87[EUR][1000 genomes]
rs927728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966176	0.90[EUR][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	nsv871097	chr1:94850443-94941890	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv546851	chr1:94916649-94941376	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv871764	chr1:94917402-95004084	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4148050	PTBP2	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94913800-94974200	Weak transcription	Psoas Muscle	Psoas
2	chr1:94914200-94951800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:94914800-94985800	Weak transcription	NHLF	lung
4	chr1:94915400-94934000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94915400-94993200	Weak transcription	HSMMtube	muscle
6	chr1:94915800-94935000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:94915800-94955400	Weak transcription	NHDF-Ad	bronchial
8	chr1:94915800-94956600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:94916000-94941800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:94916000-94957200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:94916000-94969600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:94916000-94970000	Weak transcription	Ovary	ovary
13	chr1:94916000-94970000	Weak transcription	Spleen	Spleen
14	chr1:94916000-94973800	Weak transcription	Pancreas	Pancrea
15	chr1:94916000-94993000	Weak transcription	Esophagus	oesophagus
16	chr1:94916200-94968400	Weak transcription	Gastric	stomach
17	chr1:94916200-94971600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:94916200-94974200	Weak transcription	Lung	lung
19	chr1:94917200-94964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:94917800-94971800	Weak transcription	NHEK	skin
21	chr1:94917800-95000800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:94918000-94942000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:94918000-94957000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:94918800-94941600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:94919000-94942800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:94920600-94948400	Weak transcription	Small Intestine	intestine
27	chr1:94921000-94957800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:94923200-94942000	Weak transcription	Right Ventricle	heart
29	chr1:94923600-94956400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:94923600-94956600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:94923800-94941800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:94923800-94948000	Weak transcription	NH-A	brain
33	chr1:94923800-95000400	Weak transcription	Aorta	Aorta
34	chr1:94924000-94947000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:94924000-94964400	Weak transcription	GM12878-XiMat	blood
36	chr1:94924800-94968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:94925600-94935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:94926600-94950400	Weak transcription	Primary B cells from cord blood	blood
39	chr1:94928000-94934400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:94928800-94936800	Strong transcription	HSMM	muscle
41	chr1:94929000-94938600	Weak transcription	Brain Substantia Nigra	brain
42	chr1:94929000-94954200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:94929000-94957200	Weak transcription	Colonic Mucosa	Colon
44	chr1:94929200-94938200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:94929200-94941800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:94929400-94937000	Strong transcription	Fetal Thymus	thymus
47	chr1:94929400-94941600	Weak transcription	HUVEC	blood vessel
48	chr1:94929400-94947000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:94929400-94980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:94929600-94934000	Strong transcription	Dnd41	blood

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