Variant report

Variant	rs28401668
Chromosome Location	chr4:56323414-56323415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10016977	0.90[AFR][1000 genomes]
rs11133401	0.90[AFR][1000 genomes]
rs28375674	0.90[AFR][1000 genomes]
rs28376882	0.82[AFR][1000 genomes]
rs28415334	0.86[AFR][1000 genomes]
rs28434262	0.81[AFR][1000 genomes]
rs28456193	0.90[AFR][1000 genomes]
rs28545367	0.81[AFR][1000 genomes]
rs28547142	0.90[AFR][1000 genomes]
rs28548946	0.90[AFR][1000 genomes]
rs28572326	0.80[AFR][1000 genomes]
rs28590090	0.90[AFR][1000 genomes]
rs28606621	0.90[AFR][1000 genomes]
rs28683692	0.90[AFR][1000 genomes]
rs28712413	0.90[AFR][1000 genomes]
rs34401111	0.90[AFR][1000 genomes]
rs9992424	0.81[AFR][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:56274600-56332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56290800-56340400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:56290800-56340600	Weak transcription	Thymus	Thymus
5	chr4:56293000-56324800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:56293000-56354800	Weak transcription	Aorta	Aorta
7	chr4:56294000-56341200	Weak transcription	Small Intestine	intestine
8	chr4:56301600-56334800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:56301800-56332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:56301800-56339200	Weak transcription	Fetal Brain Male	brain
11	chr4:56302400-56375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:56303000-56340200	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:56304000-56331800	Weak transcription	Esophagus	oesophagus
14	chr4:56304600-56365600	Weak transcription	Spleen	Spleen
15	chr4:56304800-56331800	Weak transcription	Gastric	stomach
16	chr4:56304800-56340000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:56304800-56375800	Weak transcription	Pancreas	Pancrea
18	chr4:56306000-56361200	Weak transcription	Stomach Mucosa	stomach
19	chr4:56307600-56340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:56308800-56340400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:56312600-56325600	Strong transcription	Liver	Liver
22	chr4:56313200-56325400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:56313400-56325400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:56313600-56328400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:56313800-56324800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:56313800-56325200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:56314200-56325800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:56314400-56325200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:56314400-56336600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:56314400-56340200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:56314400-56340800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:56314400-56356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:56314400-56377200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:56315000-56340600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:56315000-56340600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:56315200-56331800	Weak transcription	Psoas Muscle	Psoas
37	chr4:56315400-56357000	Weak transcription	Hela-S3	cervix
38	chr4:56315600-56330200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:56315600-56330400	Weak transcription	Brain Angular Gyrus	brain
40	chr4:56315800-56341000	Weak transcription	Colonic Mucosa	Colon
41	chr4:56316200-56340400	Weak transcription	Fetal Heart	heart
42	chr4:56316400-56340200	Weak transcription	Fetal Thymus	thymus
43	chr4:56317000-56340000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:56317200-56331600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:56317200-56340400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:56317800-56324800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:56317800-56340200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:56318600-56324200	Weak transcription	NH-A	brain
49	chr4:56318600-56331200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:56318600-56331800	Weak transcription	Stomach Smooth Muscle	stomach

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