Variant report

Variant	rs28754309
Chromosome Location	chr5:179473460-179473461
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179466042..179468757-chr5:179469985..179473584,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10045947	0.82[EUR][1000 genomes]
rs10054764	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10058085	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10073876	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075627	0.82[EUR][1000 genomes]
rs11948891	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115042	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404973	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405022	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73348273	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7448914	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7706876	0.92[EUR][1000 genomes]
rs9329092	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179462800-179474800	Weak transcription	Fetal Heart	heart
5	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
6	chr5:179463600-179475600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
8	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:179464400-179476800	Weak transcription	HepG2	liver
11	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:179464600-179473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:179464600-179473800	Weak transcription	Right Ventricle	heart
14	chr5:179464600-179474400	Weak transcription	Primary T cells from cord blood	blood
15	chr5:179464800-179473800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:179465200-179474800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:179465200-179474800	Weak transcription	Psoas Muscle	Psoas
19	chr5:179465200-179475800	Weak transcription	HSMMtube	muscle
20	chr5:179465400-179473600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:179465400-179474600	Weak transcription	Lung	lung
22	chr5:179465400-179477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
24	chr5:179465600-179474800	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:179467400-179474600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:179467400-179474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:179467400-179483200	Weak transcription	HSMM	muscle
28	chr5:179467600-179473600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:179467600-179473600	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:179467600-179474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:179467600-179474800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:179467800-179474800	Weak transcription	Left Ventricle	heart
33	chr5:179467800-179474800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:179467800-179475800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:179467800-179479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:179468000-179474800	Weak transcription	Liver	Liver
37	chr5:179468200-179477400	Weak transcription	A549	lung
38	chr5:179468600-179473600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:179468800-179475600	Weak transcription	Gastric	stomach
40	chr5:179469000-179477000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:179470600-179475600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:179470800-179473600	Weak transcription	Adipose Nuclei	Adipose
43	chr5:179470800-179474400	Weak transcription	Ovary	ovary
44	chr5:179471000-179475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:179471200-179475400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:179471400-179476400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:179471800-179473800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr5:179471800-179474000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:179471800-179474000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr5:179471800-179475800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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