Variant report

Variant	rs56759227
Chromosome Location	chr1:180398943-180398944
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10914021	0.83[EUR][1000 genomes]
rs10914022	0.81[EUR][1000 genomes]
rs13373944	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13374104	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13374665	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376342	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1416822	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17300282	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17300340	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17300600	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17300712	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17372281	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17372295	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17372362	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17372667	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28816398	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4405110	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4446932	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4651065	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57537558	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57882351	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58047798	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58677059	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59022209	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59113753	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59829460	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60927564	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6425643	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6672501	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6680668	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694896	0.91[EUR][1000 genomes]
rs6702245	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704001	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72712995	0.90[EUR][1000 genomes]
rs72713000	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72714804	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72714834	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72714847	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714855	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714856	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714861	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714864	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714870	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714877	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714879	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714887	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714902	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72716607	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716615	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716616	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716625	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716627	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72716629	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716632	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72720914	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74132851	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74135185	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7517775	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525689	0.82[EUR][1000 genomes]
rs946636	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs961162	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9650999	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180341200-180401400	Weak transcription	Osteobl	bone
2	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
3	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
4	chr1:180355200-180402600	Weak transcription	HMEC	breast
5	chr1:180356800-180406200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:180356800-180407000	Weak transcription	Aorta	Aorta
7	chr1:180361400-180407600	Weak transcription	HepG2	liver
8	chr1:180364400-180401600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:180364600-180401000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:180365000-180401000	Weak transcription	Ovary	ovary
11	chr1:180365200-180420600	Weak transcription	A549	lung
12	chr1:180365400-180402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:180374600-180404000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:180376200-180407400	Weak transcription	NHLF	lung
15	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:180379800-180406000	Weak transcription	Left Ventricle	heart
17	chr1:180380400-180401000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:180380400-180408000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:180381200-180402800	Weak transcription	NHEK	skin
20	chr1:180381200-180406400	Weak transcription	Fetal Stomach	stomach
21	chr1:180381400-180401000	Weak transcription	HSMM	muscle
22	chr1:180382400-180401000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:180382400-180410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:180382600-180400800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:180382600-180402800	Weak transcription	Placenta	Placenta
26	chr1:180382600-180406000	Weak transcription	Dnd41	blood
27	chr1:180382600-180406400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:180382600-180406600	Weak transcription	Hela-S3	cervix
29	chr1:180385600-180401600	Weak transcription	Fetal Kidney	kidney
30	chr1:180389600-180406000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:180389800-180410400	Weak transcription	Fetal Intestine Large	intestine
32	chr1:180390200-180401600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:180391000-180409000	Weak transcription	Primary T cells from cord blood	blood
34	chr1:180391200-180410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:180391400-180404800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:180391600-180403800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:180391800-180402800	Weak transcription	Fetal Intestine Small	intestine
38	chr1:180391800-180404000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:180391800-180408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:180392000-180403000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:180392200-180405400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:180392600-180446200	Weak transcription	K562	blood
43	chr1:180394400-180407000	Weak transcription	Psoas Muscle	Psoas
44	chr1:180394400-180407800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:180394600-180405000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:180394600-180407000	Weak transcription	Brain Germinal Matrix	brain
47	chr1:180394800-180401600	Weak transcription	NHDF-Ad	bronchial
48	chr1:180394800-180403000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:180394800-180420200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:180395800-180400000	Weak transcription	Fetal Muscle Trunk	muscle

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