Variant report

Variant	rs28564509
Chromosome Location	chr4:53768812-53768813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10004829	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014061	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014144	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030623	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034233	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049923	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331609	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167293	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698672	0.83[ASN][1000 genomes]
rs2086727	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200225	0.83[ASN][1000 genomes]
rs28432778	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454037	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472535	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28491101	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508082	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610009	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615713	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28678012	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690295	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28786135	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930104	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930105	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930106	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301098	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301099	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301103	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301104	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301113	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301114	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301116	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458513	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833350	0.83[ASN][1000 genomes]
rs6855240	0.83[ASN][1000 genomes]
rs7658319	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677726	0.83[ASN][1000 genomes]
rs7680614	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996166	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9998405	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
2	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:53735000-53770200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr4:53735200-53778000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:53735800-53772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:53736600-53785600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:53737200-53779200	Weak transcription	Gastric	stomach
8	chr4:53743400-53771000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:53743600-53770200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:53750200-53770000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:53750400-53769400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:53750600-53769400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:53757000-53781200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:53759000-53769200	Weak transcription	Fetal Lung	lung
15	chr4:53760000-53773600	Weak transcription	NHLF	lung
16	chr4:53761000-53778000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:53761000-53788000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:53761200-53769200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:53761400-53775000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:53761800-53778000	Weak transcription	NHEK	skin
21	chr4:53766600-53780600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:53766800-53777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:53767200-53769000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:53767400-53771400	Weak transcription	HSMMtube	muscle
25	chr4:53767400-53774800	Strong transcription	Primary T cells from cord blood	blood
26	chr4:53767600-53770400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:53767600-53770600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:53767600-53770600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:53767600-53770600	Weak transcription	Adipose Nuclei	Adipose
30	chr4:53767600-53789000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:53767800-53769400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:53767800-53769600	Strong transcription	Dnd41	blood
33	chr4:53767800-53772000	Weak transcription	Thymus	Thymus
34	chr4:53767800-53773000	Weak transcription	Fetal Stomach	stomach
35	chr4:53767800-53778000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:53767800-53782000	Weak transcription	Aorta	Aorta
37	chr4:53768000-53769600	Strong transcription	Primary B cells from cord blood	blood
38	chr4:53768000-53782000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:53768200-53769000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr4:53768200-53774400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr4:53768200-53779000	Weak transcription	Ovary	ovary
42	chr4:53768200-53779800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:53768400-53769400	Weak transcription	Lung	lung
44	chr4:53768400-53774600	Weak transcription	GM12878-XiMat	blood
45	chr4:53768400-53778000	Weak transcription	Fetal Intestine Small	intestine
46	chr4:53768400-53779000	Weak transcription	Liver	Liver
47	chr4:53768400-53779000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:53768400-53782000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:53768600-53770600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:53768600-53770600	Weak transcription	Fetal Muscle Leg	muscle

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