Variant report

Variant	rs2296382
Chromosome Location	chr1:94971863-94971864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94965266..94968110-chr1:94970843..94972625,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

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];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1034363	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1041282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165149	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11576665	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11581292	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582033	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1158254	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11585880	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12120731	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130330	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12131298	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12143221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12143512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16946	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[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];0.87[ASN][1000 genomes]
rs17410399	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2050648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2147794	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2794470	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4148042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148050	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]
rs4148052	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4148056	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];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148060	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536006	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4847303	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55801886	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56353982	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61772847	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61772851	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61772854	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61772857	0.86[ASN][1000 genomes]
rs698950	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7555399	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs841692	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs841695	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs927728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs966176	0.95[EUR][1000 genomes];0.85[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	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
2	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv947290	chr1:94970084-94984156	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296382	PTBP2	cis	cerebellum	SCAN

Chromatin state (count:111 , 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	chr1:94914800-94985800	Weak transcription	NHLF	lung
3	chr1:94915400-94993200	Weak transcription	HSMMtube	muscle
4	chr1:94916000-94973800	Weak transcription	Pancreas	Pancrea
5	chr1:94916000-94993000	Weak transcription	Esophagus	oesophagus
6	chr1:94916200-94974200	Weak transcription	Lung	lung
7	chr1:94917800-95000800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:94923800-95000400	Weak transcription	Aorta	Aorta
9	chr1:94929400-94980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:94929600-94985400	Weak transcription	Fetal Brain Female	brain
11	chr1:94930800-94974000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:94942400-94997200	Weak transcription	Right Ventricle	heart
13	chr1:94946400-94993000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:94952800-94987800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:94952800-94993000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:94952800-94993400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:94956200-95004000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:94956600-94987200	Weak transcription	Fetal Heart	heart
19	chr1:94958000-94985400	Weak transcription	Fetal Brain Male	brain
20	chr1:94958400-94972800	Weak transcription	Brain Germinal Matrix	brain
21	chr1:94958400-94982600	Weak transcription	HMEC	breast
22	chr1:94958400-94992200	Weak transcription	NHDF-Ad	bronchial
23	chr1:94958400-94993200	Weak transcription	NH-A	brain
24	chr1:94958600-94976800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:94958600-94987600	Weak transcription	Primary B cells from cord blood	blood
26	chr1:94958600-95004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:94960600-94973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:94962000-94988000	Weak transcription	HUVEC	blood vessel
29	chr1:94963200-94972200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:94963200-94972400	Strong transcription	Liver	Liver
31	chr1:94963800-94972200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:94963800-94972400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:94963800-94972400	Strong transcription	Primary T cells from cord blood	blood
34	chr1:94964000-94972200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:94964000-94972400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:94964000-94972400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:94964000-94972400	Strong transcription	Dnd41	blood
38	chr1:94964200-94972400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:94964200-94972400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:94964400-94972400	Strong transcription	Fetal Intestine Large	intestine
41	chr1:94965000-94975200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:94965400-94987800	Weak transcription	GM12878-XiMat	blood
43	chr1:94965400-94995800	Weak transcription	HSMM	muscle
44	chr1:94965600-94972400	Strong transcription	Thymus	Thymus
45	chr1:94965600-94982000	Weak transcription	Stomach Mucosa	stomach
46	chr1:94965600-94988200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:94965600-95000400	Weak transcription	Small Intestine	intestine
48	chr1:94965600-95006400	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:94965800-94977600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:94966200-94993000	Weak transcription	Hela-S3	cervix

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