Variant report

Variant	rs56376445
Chromosome Location	chr1:180380242-180380243
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1072856	1.00[EUR][1000 genomes]
rs16855661	1.00[EUR][1000 genomes]
rs16855695	1.00[EUR][1000 genomes]
rs16855749	1.00[EUR][1000 genomes]
rs16855769	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855834	1.00[EUR][1000 genomes]
rs16855837	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16855850	1.00[EUR][1000 genomes]
rs16855855	1.00[EUR][1000 genomes]
rs16855910	1.00[EUR][1000 genomes]
rs16855982	1.00[EUR][1000 genomes]
rs16855986	1.00[EUR][1000 genomes]
rs16855990	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856007	1.00[EUR][1000 genomes]
rs16856037	1.00[EUR][1000 genomes]
rs16856064	1.00[EUR][1000 genomes]
rs2764456	0.85[AFR][1000 genomes]
rs2764458	0.91[AFR][1000 genomes]
rs4333819	0.85[AFR][1000 genomes]
rs4590641	1.00[EUR][1000 genomes]
rs55675122	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55698496	1.00[EUR][1000 genomes]
rs55719709	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55754938	1.00[EUR][1000 genomes]
rs56005059	1.00[EUR][1000 genomes]
rs56089354	1.00[EUR][1000 genomes]
rs56128856	1.00[EUR][1000 genomes]
rs56233435	1.00[EUR][1000 genomes]
rs56246577	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57451284	1.00[EUR][1000 genomes]
rs57948698	1.00[EUR][1000 genomes]
rs58175505	1.00[EUR][1000 genomes]
rs59612061	1.00[EUR][1000 genomes]
rs60088677	1.00[EUR][1000 genomes]
rs60300532	1.00[EUR][1000 genomes]
rs60439251	1.00[EUR][1000 genomes]
rs60509208	1.00[EUR][1000 genomes]
rs60729009	1.00[EUR][1000 genomes]
rs60923108	1.00[EUR][1000 genomes]
rs60993519	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61057572	1.00[EUR][1000 genomes]
rs61700262	1.00[EUR][1000 genomes]
rs6425623	0.82[AFR][1000 genomes]
rs6425639	0.92[AFR][1000 genomes]
rs6672551	1.00[EUR][1000 genomes]
rs6675201	1.00[EUR][1000 genomes]
rs6675208	1.00[EUR][1000 genomes]
rs74132455	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74132456	1.00[EUR][1000 genomes]
rs74132457	1.00[EUR][1000 genomes]
rs74132463	1.00[EUR][1000 genomes]
rs74132465	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132472	1.00[EUR][1000 genomes]
rs74132476	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74132478	1.00[EUR][1000 genomes]
rs74132903	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132904	1.00[EUR][1000 genomes]
rs74132915	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132919	1.00[EUR][1000 genomes]
rs74132933	1.00[EUR][1000 genomes]
rs74135059	1.00[EUR][1000 genomes]
rs74135188	1.00[EUR][1000 genomes]
rs7518809	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518923	1.00[EUR][1000 genomes]
rs7520598	1.00[EUR][1000 genomes]
rs7536470	1.00[EUR][1000 genomes]
rs7537732	1.00[EUR][1000 genomes]
rs7548328	1.00[EUR][1000 genomes]
rs9659140	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:106 , 50 per page) page: 1 2 3

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	chr1:180352400-180381400	Weak transcription	Hela-S3	cervix
5	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
6	chr1:180354800-180386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:180355200-180402600	Weak transcription	HMEC	breast
8	chr1:180355600-180390800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:180356600-180381400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:180356600-180394000	Weak transcription	NHDF-Ad	bronchial
11	chr1:180356800-180380800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:180356800-180406200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:180356800-180407000	Weak transcription	Aorta	Aorta
14	chr1:180360400-180394200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:180361000-180381000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:180361000-180383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:180361400-180407600	Weak transcription	HepG2	liver
18	chr1:180361600-180382800	Weak transcription	Liver	Liver
19	chr1:180363400-180385200	Weak transcription	Fetal Kidney	kidney
20	chr1:180364000-180394200	Weak transcription	HSMMtube	muscle
21	chr1:180364400-180381600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:180364400-180383400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:180364400-180384200	Weak transcription	Brain Anterior Caudate	brain
24	chr1:180364400-180392800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:180364400-180401600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:180364600-180380800	Weak transcription	Fetal Stomach	stomach
27	chr1:180364600-180401000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:180364800-180383800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:180364800-180390200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:180365000-180391200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:180365000-180401000	Weak transcription	Ovary	ovary
32	chr1:180365200-180381000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:180365200-180390200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:180365200-180420600	Weak transcription	A549	lung
35	chr1:180365400-180380600	Weak transcription	K562	blood
36	chr1:180365400-180402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:180365600-180384600	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:180366200-180390200	Weak transcription	Fetal Brain Male	brain
39	chr1:180366600-180393600	Weak transcription	NH-A	brain
40	chr1:180366800-180380600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:180366800-180394000	Weak transcription	Fetal Lung	lung
42	chr1:180369600-180385000	Weak transcription	HUVEC	blood vessel
43	chr1:180370600-180391400	Weak transcription	Lung	lung
44	chr1:180371200-180394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:180373000-180380600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:180373000-180381000	Weak transcription	NHEK	skin
47	chr1:180373400-180380600	Weak transcription	Fetal Intestine Small	intestine
48	chr1:180373600-180384400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:180374400-180384400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:180374600-180394200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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