Variant report

Variant	rs28542460
Chromosome Location	chr6:161542395-161542396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10080366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11966001	1.00[EUR][1000 genomes]
rs12181932	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12333168	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13437252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16892148	1.00[AMR][1000 genomes]
rs16892155	1.00[AMR][1000 genomes]
rs16892160	1.00[AMR][1000 genomes]
rs16892171	1.00[AMR][1000 genomes]
rs1822519	1.00[EUR][1000 genomes]
rs28493041	0.83[EUR][1000 genomes]
rs58963158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6455705	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901507	1.00[EUR][1000 genomes]
rs6907956	0.84[AFR][1000 genomes]
rs6922585	1.00[EUR][1000 genomes]
rs6928749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6934713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6935472	1.00[EUR][1000 genomes]
rs6935813	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6936925	1.00[EUR][1000 genomes]
rs6937754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015405	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73015418	0.83[EUR][1000 genomes]
rs73015443	0.83[EUR][1000 genomes]
rs73015456	0.83[EUR][1000 genomes]
rs73022077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73022082	1.00[EUR][1000 genomes]
rs73022084	0.86[EUR][1000 genomes]
rs73022090	1.00[EUR][1000 genomes]
rs73022096	1.00[EUR][1000 genomes]
rs73023854	0.83[EUR][1000 genomes]
rs73023856	0.83[EUR][1000 genomes]
rs73023871	1.00[EUR][1000 genomes]
rs73024033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73024041	1.00[EUR][1000 genomes]
rs73024080	1.00[EUR][1000 genomes]
rs73026055	1.00[EUR][1000 genomes]
rs73026079	1.00[EUR][1000 genomes]
rs7356842	0.86[EUR][1000 genomes]
rs7356869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754196	1.00[EUR][1000 genomes]
rs7754687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7762953	1.00[EUR][1000 genomes]
rs7767689	1.00[AMR][1000 genomes]
rs7767849	1.00[AMR][1000 genomes]
rs7775116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7775538	1.00[EUR][1000 genomes]
rs9295133	1.00[EUR][1000 genomes]
rs9295135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456606	1.00[EUR][1000 genomes]
rs9456608	1.00[EUR][1000 genomes]
rs9456609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456612	1.00[AMR][1000 genomes]
rs9456613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456615	1.00[EUR][1000 genomes]
rs9456616	1.00[EUR][1000 genomes]
rs9456618	1.00[AMR][1000 genomes]
rs9456621	1.00[EUR][1000 genomes]
rs9456622	1.00[EUR][1000 genomes]
rs9456624	1.00[EUR][1000 genomes]
rs9456625	1.00[EUR][1000 genomes]
rs9456626	1.00[EUR][1000 genomes]
rs9456627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456628	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9456630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9456635	0.91[AFR][1000 genomes]
rs9456640	0.83[EUR][1000 genomes]
rs9456643	0.83[EUR][1000 genomes]
rs9458074	1.00[EUR][1000 genomes]
rs9458075	1.00[EUR][1000 genomes]
rs9458076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458079	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458080	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458081	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458089	1.00[EUR][1000 genomes]
rs9458090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458095	1.00[EUR][1000 genomes]
rs9458096	1.00[EUR][1000 genomes]
rs9458097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458105	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458111	0.86[EUR][1000 genomes]
rs9458112	1.00[EUR][1000 genomes]
rs9458113	1.00[EUR][1000 genomes]
rs9458115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458116	1.00[EUR][1000 genomes]
rs9458118	1.00[EUR][1000 genomes]
rs9458119	1.00[EUR][1000 genomes]
rs9458120	1.00[EUR][1000 genomes]
rs9458123	1.00[EUR][1000 genomes]
rs9458124	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9458125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458127	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458132	0.93[AFR][1000 genomes]
rs9458133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458134	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458161	0.83[EUR][1000 genomes]
rs9458167	0.83[EUR][1000 genomes]
rs9986548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161494400-161542400	Strong transcription	Duodenum Mucosa	Duodenum
2	chr6:161514000-161544600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:161517600-161543000	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:161522400-161542400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr6:161527000-161543000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:161527200-161542800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:161527400-161543600	Strong transcription	Fetal Lung	lung
8	chr6:161527600-161547800	Weak transcription	Right Atrium	heart
9	chr6:161528600-161544800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:161529600-161547600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:161533200-161542800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:161533200-161543400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:161533600-161543200	Strong transcription	Primary T cells from cord blood	blood
14	chr6:161533800-161542800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:161534000-161549800	Weak transcription	Stomach Mucosa	stomach
16	chr6:161534600-161547200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:161534600-161555800	Weak transcription	A549	lung
18	chr6:161534600-161559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:161536000-161543800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:161537000-161546400	Weak transcription	NH-A	brain
21	chr6:161537600-161556800	Weak transcription	Gastric	stomach
22	chr6:161537800-161548200	Weak transcription	Small Intestine	intestine
23	chr6:161538200-161543400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:161538200-161544200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:161538200-161544200	Weak transcription	Brain Angular Gyrus	brain
26	chr6:161538200-161547800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:161538200-161548000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:161538200-161548000	Weak transcription	Aorta	Aorta
29	chr6:161538200-161549400	Weak transcription	NHEK	skin
30	chr6:161538200-161559600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:161538400-161543800	Weak transcription	GM12878-XiMat	blood
32	chr6:161538400-161547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:161538400-161547800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:161538400-161548000	Weak transcription	Lung	lung
35	chr6:161538400-161549400	Weak transcription	HSMMtube	muscle
36	chr6:161538400-161553000	Weak transcription	Spleen	Spleen
37	chr6:161538400-161557800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:161538400-161558400	Weak transcription	HMEC	breast
39	chr6:161538600-161543800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:161538600-161547400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:161538600-161547400	Weak transcription	Fetal Stomach	stomach
42	chr6:161538600-161547400	Weak transcription	Thymus	Thymus
43	chr6:161538600-161547600	Weak transcription	Fetal Thymus	thymus
44	chr6:161538600-161547800	Weak transcription	Esophagus	oesophagus
45	chr6:161538600-161547800	Weak transcription	Right Ventricle	heart
46	chr6:161538600-161552600	Weak transcription	Pancreas	Pancrea
47	chr6:161538600-161554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:161538600-161555600	Weak transcription	NHLF	lung
49	chr6:161538600-161559600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:161538800-161544000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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