Variant report

Variant	rs28493963
Chromosome Location	chr5:68795498-68795499
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr5:68795412-68796481	HEK293	kidney:	n/a	n/a
2	SETDB1	chr5:68795388-68796560	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68787536..68790695-chr5:68794621..68799046,5	MCF-7	breast:
2	chr5:68787711..68790252-chr5:68793070..68796415,3	K562	blood:
3	chr5:68786861..68791714-chr5:68792845..68799561,13	MCF-7	breast:

Variant related genes	Relation type
OCLN	TF binding region
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28529133	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28659922	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34221525	0.82[EUR][1000 genomes]
rs34532558	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628909	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55818294	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56016558	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60039937	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61396502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773445	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	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1023116	chr5:68744307-68867282	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034024	chr5:68760271-69118123	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68790000-68798200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:68790200-68795800	Weak transcription	Colonic Mucosa	Colon
3	chr5:68790200-68797400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:68790200-68797400	Weak transcription	HMEC	breast
5	chr5:68790200-68797400	Weak transcription	HUVEC	blood vessel
6	chr5:68790200-68824600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:68790600-68801600	Weak transcription	Gastric	stomach
8	chr5:68790800-68798600	Weak transcription	Lung	lung
9	chr5:68791200-68798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:68791400-68798200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:68791600-68795800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:68791600-68798400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:68792800-68798000	Weak transcription	NHLF	lung
14	chr5:68792800-68798200	Weak transcription	Fetal Kidney	kidney
15	chr5:68793000-68795600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:68793000-68795600	Weak transcription	HepG2	liver
17	chr5:68793000-68795800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:68793000-68795800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:68793000-68797400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:68793000-68797600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:68793000-68798200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:68793000-68798200	Weak transcription	HSMM	muscle
23	chr5:68793200-68795800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:68793200-68795800	Weak transcription	Fetal Lung	lung
25	chr5:68793200-68796600	Weak transcription	Liver	Liver
26	chr5:68793200-68797600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:68793200-68798200	Weak transcription	GM12878-XiMat	blood
28	chr5:68793200-68798400	Weak transcription	HSMMtube	muscle
29	chr5:68793200-68813600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr5:68793400-68795600	Weak transcription	Stomach Mucosa	stomach
31	chr5:68793400-68795800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:68793400-68795800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:68793400-68801600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:68793600-68798600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:68793600-68800200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:68793600-68806000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:68794000-68796200	Enhancers	A549	lung
38	chr5:68794000-68800200	Enhancers	Fetal Intestine Large	intestine
39	chr5:68794600-68797000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr5:68794800-68797600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr5:68795000-68795800	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr5:68795000-68797600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:68795200-68795600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:68795200-68795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:68795200-68799200	Enhancers	Fetal Intestine Small	intestine
46	chr5:68795400-68795600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:68795400-68796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:68795400-68799800	Enhancers	Pancreas	Pancrea

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