Variant report

Variant	rs28868900
Chromosome Location	chr5:107708152-107708153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr5:107707667-107708752	U2OS	brain:	n/a	n/a
2	CBX3	chr5:107708074-107708501	K562	blood:	n/a	n/a
3	ZNF143	chr5:107708142-107708438	H1-hESC	embryonic stem cell:	n/a	n/a
4	TRIM28	chr5:107708052-107708438	K562	blood:	n/a	n/a
5	ZNF143	chr5:107708122-107708403	K562	blood:	n/a	n/a
6	KAP1	chr5:107707738-107708524	HEK293	kidney:	n/a	n/a
7	KAP1	chr5:107707790-107708734	K562	blood:	n/a	n/a
8	CBX3	chr5:107708110-107708382	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:393917..395827-chr5:107707504..107710114,2	MCF-7	breast:
2	chr5:107702113..107704886-chr5:107707019..107708765,2	K562	blood:
3	chr5:107705977..107708184-chr5:107711910..107713807,2	MCF-7	breast:
4	chr5:107703047..107709148-chr5:107715421..107721287,10	K562	blood:
5	chr5:107703017..107709518-chr5:107714821..107720551,7	MCF-7	breast:

No data

Variant related genes	Relation type
FBXL17	TF binding region
ENSG00000184363	Chromatin interaction
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10055785	0.81[ASN][1000 genomes]
rs10056658	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057274	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10057905	0.88[EUR][1000 genomes]
rs10070565	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10072616	0.90[ASN][1000 genomes]
rs10477889	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10477894	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13174270	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1839224	0.89[EUR][1000 genomes]
rs2044711	0.88[EUR][1000 genomes]
rs2122157	0.89[EUR][1000 genomes]
rs28584643	0.87[ASN][1000 genomes]
rs286762	0.87[EUR][1000 genomes]
rs286765	0.85[EUR][1000 genomes]
rs286766	0.85[EUR][1000 genomes]
rs2922409	0.87[EUR][1000 genomes]
rs2922410	0.88[EUR][1000 genomes]
rs2922411	0.89[EUR][1000 genomes]
rs2922413	0.89[EUR][1000 genomes]
rs2922414	0.88[EUR][1000 genomes]
rs2922415	0.88[EUR][1000 genomes]
rs2922416	0.88[EUR][1000 genomes]
rs2922419	0.89[EUR][1000 genomes]
rs2922434	0.88[EUR][1000 genomes]
rs2966794	0.89[EUR][1000 genomes]
rs2966805	0.88[EUR][1000 genomes]
rs2966806	0.89[EUR][1000 genomes]
rs2966807	0.81[EUR][1000 genomes]
rs2966808	0.89[EUR][1000 genomes]
rs2966809	0.89[EUR][1000 genomes]
rs2966810	0.89[EUR][1000 genomes]
rs2966812	0.89[EUR][1000 genomes]
rs2966815	0.88[EUR][1000 genomes]
rs2966817	0.88[EUR][1000 genomes]
rs2966819	0.88[EUR][1000 genomes]
rs34019963	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34088844	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35053804	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35624833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35959276	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756573	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs399438	0.87[EUR][1000 genomes]
rs4276393	0.89[EUR][1000 genomes]
rs4385196	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4957750	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66855775	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6860212	0.82[EUR][1000 genomes]
rs715638	0.84[EUR][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	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882688	chr5:107595383-107715746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107654600-107709400	Weak transcription	Pancreas	Pancrea
2	chr5:107658600-107709200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:107663800-107709400	Weak transcription	Primary T cells from cord blood	blood
4	chr5:107667600-107709200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:107669200-107708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:107675000-107709200	Weak transcription	Fetal Thymus	thymus
7	chr5:107677800-107709200	Weak transcription	Ovary	ovary
8	chr5:107696600-107709200	Weak transcription	Fetal Lung	lung
9	chr5:107697200-107715200	Weak transcription	HSMM	muscle
10	chr5:107697800-107709200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:107698200-107715600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:107699000-107712800	Weak transcription	Right Ventricle	heart
13	chr5:107699600-107709200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:107700600-107709000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:107700600-107709400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:107701000-107709400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:107701200-107709000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:107701200-107709400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:107702600-107709200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr5:107702600-107709200	Weak transcription	Psoas Muscle	Psoas
21	chr5:107702800-107708200	Weak transcription	Fetal Kidney	kidney
22	chr5:107703400-107709200	Weak transcription	Thymus	Thymus
23	chr5:107705000-107709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:107705000-107709200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:107705800-107709200	Weak transcription	Gastric	stomach
26	chr5:107706400-107710000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:107706400-107714200	Weak transcription	Left Ventricle	heart
28	chr5:107707400-107710400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:107707600-107708400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:107707600-107708800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:107707600-107710200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:107707600-107710200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr5:107707600-107710600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:107707800-107708600	ZNF genes & repeats	Brain Anterior Caudate	brain
35	chr5:107707800-107709200	Weak transcription	Esophagus	oesophagus
36	chr5:107707800-107709400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:107707800-107709400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:107707800-107710200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr5:107708000-107708600	ZNF genes & repeats	Brain Cingulate Gyrus	brain

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