Variant report

Variant	rs28889302
Chromosome Location	chr1:98151329-98151330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12434126	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12434144	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12435532	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12436125	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12879869	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12882679	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12896672	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12897000	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2167151	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2196442	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2196445	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2197991	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2217888	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2370976	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2370977	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2370978	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2370979	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35236866	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35310631	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35441767	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35861800	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36007297	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4899743	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4903853	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4903856	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61993110	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61993111	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61993112	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61993119	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7150974	0.92[AMR][1000 genomes];0.90[EUR][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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv830714	chr1:98025090-98229416	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv2010	chr1:98123116-98167426	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98114200-98159000	Weak transcription	NHDF-Ad	bronchial
2	chr1:98125600-98159400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:98127000-98152600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:98130800-98171800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:98132200-98152800	Weak transcription	Fetal Lung	lung
6	chr1:98134200-98158600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:98135000-98152600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:98135600-98159000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:98136200-98161000	Weak transcription	Lung	lung
10	chr1:98136200-98188800	Weak transcription	Left Ventricle	heart
11	chr1:98136600-98162800	Weak transcription	Esophagus	oesophagus
12	chr1:98140600-98159000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:98141200-98165000	Weak transcription	HSMM	muscle
14	chr1:98141600-98165800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:98141800-98166000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:98141800-98185400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:98142400-98161200	Weak transcription	Aorta	Aorta
18	chr1:98142800-98155200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:98143000-98159000	Weak transcription	Thymus	Thymus
20	chr1:98143200-98158600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:98143600-98153400	Weak transcription	Pancreas	Pancrea
22	chr1:98143600-98165800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:98144000-98153000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:98144000-98161200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:98144000-98165400	Weak transcription	Brain Substantia Nigra	brain
26	chr1:98144000-98176600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:98144200-98152600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:98144200-98152600	Weak transcription	Ovary	ovary
29	chr1:98144200-98153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:98144200-98157800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:98144200-98158800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:98144200-98163200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:98144200-98165800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:98144200-98166800	Weak transcription	Osteobl	bone
35	chr1:98144400-98156600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:98144400-98156800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:98144400-98159000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:98144800-98162800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:98146000-98165400	Weak transcription	HMEC	breast
40	chr1:98146400-98156800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:98146400-98166800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:98146800-98152600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:98146800-98166000	Weak transcription	Adipose Nuclei	Adipose
44	chr1:98147000-98154800	Weak transcription	Fetal Intestine Large	intestine
45	chr1:98147000-98160800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:98148000-98152600	Weak transcription	Dnd41	blood
47	chr1:98148000-98156400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:98148000-98158400	Weak transcription	Spleen	Spleen
49	chr1:98148000-98159200	Weak transcription	Primary B cells from cord blood	blood
50	chr1:98148000-98192800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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