Variant report

Variant	rs60509208
Chromosome Location	chr1:180431213-180431214
allele	A/C
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: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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855850	0.89[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855982	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855986	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855990	1.00[EUR][1000 genomes]
rs16856007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856037	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856064	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4590641	0.93[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]
rs55754938	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56005059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56089354	0.97[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	0.97[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	1.00[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59566983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59612061	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60088677	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60300532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60439251	1.00[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	0.97[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	0.81[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6675208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132445	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132456	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132457	0.83[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132478	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132803	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132903	1.00[EUR][1000 genomes]
rs74132904	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132915	1.00[EUR][1000 genomes]
rs74132919	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132933	1.00[EUR][1000 genomes]
rs74135059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74135188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518809	1.00[EUR][1000 genomes]
rs7518923	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7520598	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536470	0.88[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9659140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180392600-180446200	Weak transcription	K562	blood
2	chr1:180403400-180448000	Weak transcription	HMEC	breast
3	chr1:180404200-180431800	Weak transcription	NHEK	skin
4	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
5	chr1:180421000-180431800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:180421000-180448000	Weak transcription	HSMM	muscle
7	chr1:180421200-180431400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:180421200-180431800	Weak transcription	A549	lung
9	chr1:180421200-180451600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:180425600-180431400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:180425800-180457600	Weak transcription	Aorta	Aorta
12	chr1:180426600-180431600	Weak transcription	Dnd41	blood
13	chr1:180426800-180431400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:180427400-180448200	Weak transcription	Osteobl	bone
15	chr1:180428000-180470000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:180428600-180438000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:180429400-180431400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr1:180429400-180435200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:180429600-180431400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr1:180429600-180444600	Weak transcription	Esophagus	oesophagus
21	chr1:180429600-180455000	Weak transcription	Left Ventricle	heart
22	chr1:180429800-180431600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr1:180430200-180431800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:180430200-180432600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:180430200-180454600	Weak transcription	Thymus	Thymus
26	chr1:180430400-180431400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:180430400-180431400	ZNF genes & repeats	Fetal Stomach	stomach
28	chr1:180430400-180431800	ZNF genes & repeats	Fetal Lung	lung
29	chr1:180430400-180432000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:180430600-180431600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:180430600-180431600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr1:180430600-180431600	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr1:180430600-180432200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:180430800-180431400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:180431000-180431600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr1:180431000-180431600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:180431000-180432000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr1:180431000-180432000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr1:180431000-180432200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:180431200-180431400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:180431200-180431400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
42	chr1:180431200-180432000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
43	chr1:180431200-180432000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:180431200-180432400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr1:180431200-180432800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:180431200-180435200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr1:180431200-180470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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