Variant report

Variant	rs28558226
Chromosome Location	chr4:48577121-48577122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48573447..48576202-chr4:48576256..48578868,3	K562	blood:
2	chr4:48576864..48578418-chr4:48583302..48585934,2	K562	blood:
3	chr4:48556937..48558683-chr4:48576699..48578882,2	MCF-7	breast:
4	chr4:48573447..48576202-chr4:48576256..48578192,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10805172	0.92[AFR][1000 genomes]
rs10938535	0.90[AFR][1000 genomes]
rs1616561	0.90[AFR][1000 genomes]
rs1702796	0.90[AFR][1000 genomes]
rs28371079	0.90[AFR][1000 genomes]
rs2940319	0.90[AFR][1000 genomes]
rs4235155	0.90[AFR][1000 genomes]
rs4235157	0.92[AFR][1000 genomes]
rs4694896	0.81[AFR][1000 genomes]
rs4695385	0.90[AFR][1000 genomes]
rs6823351	0.90[AFR][1000 genomes]
rs6827481	0.90[AFR][1000 genomes]
rs6848222	0.90[AFR][1000 genomes]
rs6848417	0.90[AFR][1000 genomes]
rs6853876	0.85[AFR][1000 genomes]
rs7664507	0.90[AFR][1000 genomes]
rs7689293	0.90[AFR][1000 genomes]
rs776603	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48499000-48578800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:48499600-48581400	Strong transcription	Dnd41	blood
5	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48501400-48578600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
8	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:48540600-48580400	Strong transcription	Fetal Intestine Large	intestine
11	chr4:48541000-48580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:48541000-48587800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr4:48541400-48581200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr4:48541600-48581400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:48541800-48579800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr4:48542800-48604400	Weak transcription	A549	lung
18	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:48546400-48596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:48546600-48578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:48547400-48578800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:48547400-48593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:48555000-48578200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:48556000-48581400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:48556800-48578400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:48559800-48604400	Weak transcription	HepG2	liver
28	chr4:48560800-48578800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:48561200-48581200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:48561400-48604400	Weak transcription	Stomach Mucosa	stomach
31	chr4:48562600-48596600	Weak transcription	Fetal Brain Male	brain
32	chr4:48562800-48590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:48563200-48587000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:48563400-48593600	Weak transcription	Spleen	Spleen
37	chr4:48564000-48578400	Weak transcription	Gastric	stomach
38	chr4:48564800-48578600	Strong transcription	Fetal Thymus	thymus
39	chr4:48566000-48578400	Weak transcription	Fetal Kidney	kidney
40	chr4:48566600-48587600	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:48568600-48578200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:48571400-48578600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:48571800-48578200	Strong transcription	Liver	Liver
44	chr4:48571800-48578600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:48572200-48578000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:48572400-48578000	Weak transcription	Aorta	Aorta
47	chr4:48572400-48578000	Weak transcription	Fetal Stomach	stomach
48	chr4:48572600-48577200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:48572600-48582600	Weak transcription	Brain Germinal Matrix	brain
50	chr4:48573200-48586200	Weak transcription	Psoas Muscle	Psoas

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