Variant report

Variant	rs28688345
Chromosome Location	chr1:86841050-86841051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11161808	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12022446	0.83[AMR][1000 genomes]
rs12023726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023799	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12029568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12030666	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12032435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12037028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037391	0.83[AMR][1000 genomes]
rs12038144	0.83[AMR][1000 genomes]
rs12038844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12042822	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12043873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044970	0.83[AMR][1000 genomes]
rs12045012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045465	0.83[AMR][1000 genomes]
rs12046199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12046894	0.83[AMR][1000 genomes]
rs12047304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047305	0.95[ASN][1000 genomes]
rs12047913	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12048082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747430	0.84[ASN][1000 genomes]
rs2274999	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28788025	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34204564	0.97[ASN][1000 genomes]
rs3737671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3765509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820038	0.83[AMR][1000 genomes]
rs4497186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55857117	0.84[ASN][1000 genomes]
rs57955693	0.84[ASN][1000 genomes]
rs58658794	0.84[ASN][1000 genomes]
rs59775624	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1793594	chr1:86833653-86858957	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
3	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
4	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
6	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
10	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:86819800-86842200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:86819800-86842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:86819800-86843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:86819800-86843000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:86820200-86841200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:86820200-86842600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:86820200-86843400	Weak transcription	Left Ventricle	heart
18	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
20	chr1:86820400-86842400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:86820400-86842800	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:86820400-86842800	Weak transcription	Placenta	Placenta
23	chr1:86820400-86845400	Weak transcription	Hela-S3	cervix
24	chr1:86820400-86846200	Weak transcription	NHLF	lung
25	chr1:86820400-86846400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:86820400-86847000	Weak transcription	Liver	Liver
27	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:86820400-86860200	Weak transcription	NHEK	skin
29	chr1:86820600-86842800	Weak transcription	Brain Substantia Nigra	brain
30	chr1:86820600-86843000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:86820600-86848000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:86820800-86842000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:86822400-86846200	Weak transcription	Gastric	stomach
34	chr1:86823000-86843000	Weak transcription	Ovary	ovary
35	chr1:86824000-86841400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:86824000-86843000	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:86824000-86848200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:86825600-86842800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:86826400-86842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:86828800-86842800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:86828800-86842800	Weak transcription	Fetal Stomach	stomach
42	chr1:86829200-86842800	Weak transcription	Fetal Brain Female	brain
43	chr1:86836400-86842800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
45	chr1:86837200-86842800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:86838200-86842000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:86838200-86842800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:86838200-86843600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:86838200-86845800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:86838400-86841200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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