Variant report

Variant	rs927728
Chromosome Location	chr1:94929485-94929486
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94526680..94527603-chr1:94928967..94929584,2	K562	blood:
2	chr1:94883768..94885488-chr1:94926929..94929559,2	MCF-7	breast:
3	chr1:94510948..94511922-chr1:94929239..94929819,2	K562	blood:
4	chr1:94883223..94885583-chr1:94928116..94929855,2	MCF-7	breast:
5	chr1:94816155..94817816-chr1:94928944..94931018,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117528	Chromatin interaction
ENSG00000198691	Chromatin interaction

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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165149	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11576665	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11581292	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11582033	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158254	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585880	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12120731	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127355	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130330	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12131298	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12143221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16946	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17410399	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147794	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296382	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]
rs2794470	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148042	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4148050	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]
rs4148052	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148060	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4536006	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4847303	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801886	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56353982	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61772847	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61772851	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61772854	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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]
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
rs927728	PTBP2	cis	cerebellum	SCAN

Chromatin state (count:117 , 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	chr1:94915400-94929800	Weak transcription	Hela-S3	cervix
5	chr1:94915400-94930400	Weak transcription	Brain Anterior Caudate	brain
6	chr1:94915400-94934000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:94915400-94993200	Weak transcription	HSMMtube	muscle
8	chr1:94915800-94930600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:94915800-94935000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:94915800-94955400	Weak transcription	NHDF-Ad	bronchial
11	chr1:94915800-94956600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:94916000-94930000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:94916000-94932000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:94916000-94941800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:94916000-94957200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:94916000-94969600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:94916000-94970000	Weak transcription	Ovary	ovary
18	chr1:94916000-94970000	Weak transcription	Spleen	Spleen
19	chr1:94916000-94973800	Weak transcription	Pancreas	Pancrea
20	chr1:94916000-94993000	Weak transcription	Esophagus	oesophagus
21	chr1:94916200-94968400	Weak transcription	Gastric	stomach
22	chr1:94916200-94971600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:94916200-94974200	Weak transcription	Lung	lung
24	chr1:94916400-94930000	Weak transcription	Osteobl	bone
25	chr1:94917200-94964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:94917600-94930000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:94917800-94971800	Weak transcription	NHEK	skin
28	chr1:94917800-95000800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:94918000-94929800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:94918000-94942000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:94918000-94957000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:94918200-94930400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:94918800-94941600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:94919000-94942800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:94920600-94948400	Weak transcription	Small Intestine	intestine
36	chr1:94920800-94930400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:94921000-94957800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:94922400-94930400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:94923000-94932000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:94923200-94942000	Weak transcription	Right Ventricle	heart
41	chr1:94923400-94929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:94923400-94930000	Weak transcription	Fetal Intestine Small	intestine
43	chr1:94923600-94930000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:94923600-94956400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:94923600-94956600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:94923800-94930000	Weak transcription	Left Ventricle	heart
47	chr1:94923800-94941800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:94923800-94948000	Weak transcription	NH-A	brain
49	chr1:94923800-95000400	Weak transcription	Aorta	Aorta
50	chr1:94924000-94930400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links