Variant report

Variant	rs55754938
Chromosome Location	chr1:180365016-180365017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1072856	1.00[EUR][1000 genomes]
rs16855661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855695	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855749	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855769	1.00[EUR][1000 genomes]
rs16855834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855850	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855855	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855910	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855982	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855986	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855990	1.00[EUR][1000 genomes]
rs16856007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856037	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856064	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4590641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55675122	1.00[EUR][1000 genomes]
rs55698496	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55719709	1.00[EUR][1000 genomes]
rs56005059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56089354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56128856	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56233435	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56246577	1.00[EUR][1000 genomes]
rs56376445	1.00[EUR][1000 genomes]
rs57451284	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57948698	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58175505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59566983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59612061	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60088677	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60300532	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60439251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60509208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60729009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60923108	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60993519	1.00[EUR][1000 genomes]
rs61057572	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61700262	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6672551	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6675201	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6675208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132445	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132456	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132457	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132463	1.00[EUR][1000 genomes]
rs74132465	1.00[EUR][1000 genomes]
rs74132472	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132478	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132803	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132903	1.00[EUR][1000 genomes]
rs74132904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132915	1.00[EUR][1000 genomes]
rs74132919	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132933	1.00[EUR][1000 genomes]
rs74135059	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74135188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518809	1.00[EUR][1000 genomes]
rs7518923	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7520598	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536470	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537732	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7548328	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9659140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
8	nsv1009742	chr1:180342203-180385459	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1014937	chr1:180360900-180399555	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180341200-180401400	Weak transcription	Osteobl	bone
2	chr1:180348200-180382600	Weak transcription	Pancreas	Pancrea
3	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
4	chr1:180351600-180378400	Weak transcription	HSMM	muscle
5	chr1:180352400-180381400	Weak transcription	Hela-S3	cervix
6	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
7	chr1:180354600-180374000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:180354800-180386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:180355200-180402600	Weak transcription	HMEC	breast
10	chr1:180355400-180378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:180355600-180378400	Weak transcription	Placenta	Placenta
12	chr1:180355600-180390800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:180356600-180381400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:180356600-180394000	Weak transcription	NHDF-Ad	bronchial
15	chr1:180356800-180373000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:180356800-180378600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:180356800-180378800	Weak transcription	Left Ventricle	heart
18	chr1:180356800-180380800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:180356800-180406200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:180356800-180407000	Weak transcription	Aorta	Aorta
21	chr1:180357000-180378400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:180357800-180366600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:180358200-180374000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:180360200-180378000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:180360400-180394200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:180361000-180365200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:180361000-180378600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:180361000-180381000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:180361000-180383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:180361400-180407600	Weak transcription	HepG2	liver
31	chr1:180361600-180382800	Weak transcription	Liver	Liver
32	chr1:180362600-180379200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:180363000-180365200	Strong transcription	A549	lung
34	chr1:180363400-180385200	Weak transcription	Fetal Kidney	kidney
35	chr1:180363600-180365200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:180363600-180366000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:180363600-180366800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:180363800-180366000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:180363800-180366600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:180363800-180378400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:180364000-180365400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:180364000-180365400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:180364000-180394200	Weak transcription	HSMMtube	muscle
44	chr1:180364200-180365200	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr1:180364200-180365200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:180364200-180365400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:180364200-180365400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr1:180364200-180365400	ZNF genes & repeats	Fetal Lung	lung
49	chr1:180364200-180365400	ZNF genes & repeats	GM12878-XiMat	blood
50	chr1:180364200-180365800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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