Variant report

Variant	rs28405928
Chromosome Location	chr2:47128925-47128926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47127180..47130356-chr2:47136713..47140377,4	K562	blood:
2	chr2:47122860..47125506-chr2:47127308..47129361,2	K562	blood:
3	chr2:47127485..47129100-chr2:47135293..47137102,2	MCF-7	breast:
4	chr2:47127542..47131326-chr2:47131677..47134825,5	K562	blood:
5	chr2:47127713..47130924-chr2:47141446..47144583,3	MCF-7	breast:
6	chr2:47114369..47117073-chr2:47127351..47131177,3	K562	blood:
7	chr2:47127370..47129670-chr2:47168001..47169784,2	K562	blood:
8	chr2:47126738..47129144-chr2:47143021..47145167,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10084332	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10164756	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10165085	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181411	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10186980	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11897050	0.83[EUR][1000 genomes]
rs13391660	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13398748	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13406024	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13407588	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13409489	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13417753	0.83[EUR][1000 genomes]
rs13424086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13430346	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13430703	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17035878	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17035912	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28465613	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28529158	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28612371	0.83[EUR][1000 genomes]
rs28770495	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4300885	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4314044	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4583513	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6729569	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6755386	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73926967	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73926970	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73926978	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73926980	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73926983	0.83[EUR][1000 genomes]
rs73926986	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73926988	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7577816	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7603884	0.83[EUR][1000 genomes]
rs9973769	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47106400-47131000	Weak transcription	Esophagus	oesophagus
2	chr2:47113200-47131200	Weak transcription	Aorta	Aorta
3	chr2:47116000-47133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:47116200-47133000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:47116600-47129600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:47116600-47129800	Weak transcription	Osteobl	bone
7	chr2:47116600-47131000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:47116600-47131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:47116600-47131800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:47116600-47132200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:47116600-47132400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:47116600-47132400	Weak transcription	NHEK	skin
13	chr2:47116800-47131000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:47117400-47133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:47117800-47131200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:47120000-47130800	Weak transcription	Left Ventricle	heart
18	chr2:47120000-47133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:47120800-47133000	Weak transcription	Pancreas	Pancrea
20	chr2:47121000-47132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:47121000-47132400	Weak transcription	Hela-S3	cervix
22	chr2:47121000-47132400	Weak transcription	NHDF-Ad	bronchial
23	chr2:47121200-47129800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:47123600-47131000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:47124200-47131000	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:47124400-47129600	Weak transcription	Primary B cells from cord blood	blood
27	chr2:47124400-47131000	Weak transcription	Fetal Intestine Small	intestine
28	chr2:47124800-47132400	Weak transcription	Fetal Lung	lung
29	chr2:47124800-47132800	Weak transcription	NHLF	lung
30	chr2:47125200-47131000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:47125200-47132200	Weak transcription	Dnd41	blood
32	chr2:47125400-47129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:47125400-47132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:47125400-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:47125600-47129600	Weak transcription	A549	lung
36	chr2:47125600-47130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:47125600-47131200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:47125800-47133200	Weak transcription	Spleen	Spleen
39	chr2:47126000-47129600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:47126000-47130200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:47126000-47131400	Weak transcription	Adipose Nuclei	Adipose
42	chr2:47126000-47132600	Weak transcription	HUVEC	blood vessel
43	chr2:47126000-47133200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:47126000-47137000	Weak transcription	Right Atrium	heart
45	chr2:47126200-47131000	Weak transcription	HepG2	liver
46	chr2:47126400-47129600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:47126400-47131200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:47126400-47132400	Weak transcription	Lung	lung
49	chr2:47126400-47132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:47126600-47131200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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