Variant report

Variant	rs56246577
Chromosome Location	chr1:180423666-180423667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
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	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855834	1.00[EUR][1000 genomes]
rs16855837	0.89[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	0.92[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	0.82[AFR][1000 genomes]
rs2764458	0.88[AFR][1000 genomes]
rs4333819	0.84[AFR][1000 genomes]
rs4590641	1.00[EUR][1000 genomes]
rs55675122	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55698496	1.00[EUR][1000 genomes]
rs55719709	0.92[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]
rs56376445	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	0.88[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	0.81[AFR][1000 genomes]
rs6425639	0.97[AFR][1000 genomes]
rs6672551	1.00[EUR][1000 genomes]
rs6675201	1.00[EUR][1000 genomes]
rs6675208	1.00[EUR][1000 genomes]
rs74132455	0.89[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	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132472	1.00[EUR][1000 genomes]
rs74132476	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74132478	1.00[EUR][1000 genomes]
rs74132903	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132904	1.00[EUR][1000 genomes]
rs74132915	0.92[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	0.92[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:7 , 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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:180392600-180446200	Weak transcription	K562	blood
3	chr1:180401400-180430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:180403400-180426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:180403400-180431200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:180403400-180448000	Weak transcription	HMEC	breast
7	chr1:180404200-180431800	Weak transcription	NHEK	skin
8	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
9	chr1:180413000-180429400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:180417600-180431200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:180418000-180431200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:180418400-180430800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:180419000-180426200	Weak transcription	Dnd41	blood
14	chr1:180420600-180429600	Weak transcription	Fetal Lung	lung
15	chr1:180421000-180429000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:180421000-180430400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:180421000-180430600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:180421000-180431200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:180421000-180431800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:180421000-180448000	Weak transcription	HSMM	muscle
21	chr1:180421200-180426200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:180421200-180426400	Weak transcription	GM12878-XiMat	blood
23	chr1:180421200-180427200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:180421200-180429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:180421200-180430200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:180421200-180431200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:180421200-180431200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:180421200-180431400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:180421200-180431800	Weak transcription	A549	lung
30	chr1:180421200-180451600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:180421400-180425600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:180421400-180425600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:180421400-180431000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:180421600-180426000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:180421600-180429400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:180421600-180430600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:180421600-180431200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:180421600-180431200	Weak transcription	Ovary	ovary
39	chr1:180422200-180424600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:180422200-180430600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:180422400-180424400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:180422600-180427600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:180422800-180426200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:180423000-180429400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:180423000-180430600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:180423600-180429400	Weak transcription	Fetal Stomach	stomach

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