Variant report

Variant	rs28547142
Chromosome Location	chr4:56375823-56375824
allele	C/G
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	0.81[AFR][1000 genomes]
rs11133401	0.81[AFR][1000 genomes]
rs28375674	1.00[AFR][1000 genomes]
rs28401668	0.90[AFR][1000 genomes]
rs28415334	0.95[AFR][1000 genomes]
rs28434262	0.81[AFR][1000 genomes]
rs28456193	1.00[AFR][1000 genomes]
rs28491470	0.86[AFR][1000 genomes]
rs28545367	0.81[AFR][1000 genomes]
rs28548946	1.00[AFR][1000 genomes]
rs28572326	0.90[AFR][1000 genomes]
rs28590090	1.00[AFR][1000 genomes]
rs28606621	0.81[AFR][1000 genomes]
rs28683692	0.81[AFR][1000 genomes]
rs28712413	0.81[AFR][1000 genomes]
rs34401111	1.00[AFR][1000 genomes]
rs9992424	0.90[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	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
5	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56314400-56377200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr4:56332600-56377800	Weak transcription	Gastric	stomach
3	chr4:56336000-56376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:56337400-56377000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:56341400-56385600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:56341600-56377000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:56341800-56376400	Weak transcription	Brain Substantia Nigra	brain
8	chr4:56341800-56376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:56342200-56377600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:56342400-56376600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:56342400-56378200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:56342800-56391400	Weak transcription	Psoas Muscle	Psoas
13	chr4:56344600-56378200	Weak transcription	Brain Germinal Matrix	brain
14	chr4:56355400-56377000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:56355400-56377000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:56355400-56377200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:56355400-56377400	Weak transcription	Brain Anterior Caudate	brain
18	chr4:56355400-56378000	Weak transcription	Aorta	Aorta
19	chr4:56355400-56379200	Weak transcription	Ovary	ovary
20	chr4:56355400-56379200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:56355400-56380800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:56355400-56381800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:56355400-56386200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:56355600-56377000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:56355600-56377000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:56355800-56376000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:56355800-56376000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:56356800-56376800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:56361200-56387400	Weak transcription	Left Ventricle	heart
30	chr4:56361400-56377000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:56361400-56381000	Weak transcription	Fetal Brain Male	brain
32	chr4:56361600-56377200	Weak transcription	Adipose Nuclei	Adipose
33	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:56361800-56384400	Weak transcription	Primary B cells from cord blood	blood
35	chr4:56362000-56377200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:56364600-56376800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:56366200-56376600	Weak transcription	Esophagus	oesophagus
38	chr4:56366200-56376600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:56366200-56377000	Weak transcription	Spleen	Spleen
40	chr4:56366200-56377200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:56366200-56377200	Weak transcription	Lung	lung
42	chr4:56366200-56377600	Weak transcription	Liver	Liver
43	chr4:56366200-56386400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:56366800-56377400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:56368600-56377000	Weak transcription	Right Ventricle	heart
46	chr4:56369400-56376200	Weak transcription	Fetal Thymus	thymus
47	chr4:56369600-56376800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:56369600-56377000	Weak transcription	Fetal Lung	lung
49	chr4:56370000-56377000	Weak transcription	HUVEC	blood vessel
50	chr4:56370000-56379200	Weak transcription	Muscle Satellite Cultured Cells	--

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