Variant report

Variant	rs6888501
Chromosome Location	chr5:52856230-52856231
allele	A/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	chr5:52856167-52857077	HEK293	kidney:	n/a	n/a
2	REST	chr5:52856014-52857419	H1-neurons	neurons:	n/a	n/a
3	CEBPB	chr5:52856056-52856712	ECC-1	luminal epithelium:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
4	GTF2F1	chr5:52856116-52857111	Hela-S3	cervix:	n/a	n/a
5	TCF12	chr5:52856012-52856944	A549	lung:	n/a	n/a
6	GATA1	chr5:52856000-52857064	PBDE	blood:	n/a	n/a
7	CEBPB	chr5:52856207-52856674	HepG2	liver:	n/a	chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
8	POLR2A	chr5:52856159-52857059	GM12892	blood:	n/a	n/a
9	CEBPB	chr5:52856168-52856539	K562	blood:	n/a	chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
10	BCLAF1	chr5:52856204-52856955	GM12878	blood:	n/a	n/a
11	CBX3	chr5:52856124-52856812	HCT-116	colon:	n/a	n/a
12	TBP	chr5:52856026-52857044	K562	blood:	n/a	n/a
13	TBL1XR1	chr5:52856196-52857073	K562	blood:	n/a	n/a
14	CEBPB	chr5:52855992-52856940	MCF-7	breast:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
15	POLR2A	chr5:52856099-52857076	PFSK-1	brain:	n/a	n/a
16	EP300	chr5:52856119-52857039	K562	blood:	n/a	chr5:52856374-52856388
17	ELF1	chr5:52856222-52856646	A549	lung:	n/a	n/a
18	YY1	chr5:52856215-52856915	ECC-1	luminal epithelium:	n/a	chr5:52856629-52856641 chr5:52856630-52856640 chr5:52856482-52856502
19	EP300	chr5:52856031-52856968	GM12878	blood:	n/a	chr5:52856374-52856388
20	POLR2A	chr5:52856196-52856998	MCF-7	breast:	n/a	n/a
21	TBP	chr5:52856208-52857041	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr5:52856114-52856800	GM12878	blood:	n/a	chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
23	POLR2A	chr5:52855999-52857194	MCF10A-Er-Src	breast:	n/a	n/a
24	TCF12	chr5:52856210-52856937	ECC-1	luminal epithelium:	n/a	n/a
25	ATF2	chr5:52856229-52856818	H1-hESC	embryonic stem cell:	n/a	n/a
26	NR2F2	chr5:52856186-52857125	K562	blood:	n/a	n/a
27	POLR2A	chr5:52856193-52857015	HepG2	liver:	n/a	n/a
28	ELF1	chr5:52856198-52857027	MCF-7	breast:	n/a	n/a
29	ELK4	chr5:52856217-52856702	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr5:52855897-52856953	A549	lung:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
31	CEBPD	chr5:52856143-52856873	K562	blood:	n/a	chr5:52856397-52856408 chr5:52856398-52856407
32	POLR2A	chr5:52856206-52856986	Gliobla	brain:	n/a	n/a
33	CEBPB	chr5:52855917-52856982	Hela-S3	cervix:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
34	ZNF143	chr5:52856209-52856966	GM12878	blood:	n/a	n/a
35	YY1	chr5:52856168-52857106	SK-N-SH	brain:	n/a	chr5:52856629-52856641 chr5:52856630-52856640 chr5:52856482-52856502
36	MAX	chr5:52855984-52857012	Hela-S3	cervix:	n/a	chr5:52856953-52856964
37	RELA	chr5:52856153-52857048	GM19099	blood:	n/a	n/a
38	MYBL2	chr5:52856134-52856761	HepG2	liver:	n/a	n/a
39	WRNIP1	chr5:52856028-52857030	GM12878	blood:	n/a	n/a
40	GABPA	chr5:52856188-52856653	A549	lung:	n/a	n/a
41	RELA	chr5:52856063-52857101	GM18505	blood:	n/a	n/a
42	TBL1XR1	chr5:52856083-52856989	GM12878	blood:	n/a	n/a
43	TCF7L2	chr5:52856180-52856857	HEK293	kidney:	n/a	n/a
44	YY1	chr5:52856015-52857151	SK-N-SH	brain:	n/a	chr5:52856629-52856641 chr5:52856630-52856640 chr5:52856482-52856502
45	POLR2A	chr5:52856177-52857121	PBDE	blood:	n/a	n/a
46	JUND	chr5:52856131-52857092	K562	blood:	n/a	chr5:52856434-52856443
47	CEBPB	chr5:52856097-52856670	A549	lung:	n/a	chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
48	POLR2A	chr5:52856205-52857041	Hela-S3	cervix:	n/a	n/a
49	CEBPB	chr5:52855935-52856730	H1-hESC	embryonic stem cell:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
50	EP300	chr5:52856229-52856701	HepG2	liver:	n/a	chr5:52856374-52856388

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:49466894..49467622-chr5:52856230..52856915,2	NB4	blood:
2	chr2:11680129..11682138-chr5:52854884..52857698,2	MCF-7	breast:

Variant related genes	Relation type
NDUFS4	TF binding region
ENSG00000264010	Chromatin interaction
ENSG00000267898	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10940325	1.00[AMR][1000 genomes]
rs11740800	1.00[YRI][hapmap]
rs11743262	0.80[YRI][hapmap]
rs16881602	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2087618	0.89[YRI][hapmap]
rs3958630	0.89[YRI][hapmap]
rs4147739	0.89[YRI][hapmap]
rs4147744	0.80[YRI][hapmap]
rs6450156	1.00[AMR][1000 genomes]
rs7700514	0.88[AFR][1000 genomes]
rs7729894	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52855600-52858200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:52855800-52856400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr5:52855800-52856400	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr5:52855800-52856400	Flanking Active TSS	Dnd41	blood
5	chr5:52855800-52856600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:52855800-52856600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:52855800-52856600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:52855800-52856600	Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr5:52855800-52856800	Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr5:52855800-52857000	Active TSS	Primary T cells from cord blood	blood
11	chr5:52855800-52857200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:52855800-52857200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr5:52855800-52857200	Active TSS	Hela-S3	cervix
14	chr5:52855800-52857400	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:52855800-52857400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:52855800-52857400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr5:52855800-52857400	Active TSS	Brain Anterior Caudate	brain
18	chr5:52855800-52857400	Active TSS	Brain Cingulate Gyrus	brain
19	chr5:52855800-52857400	Active TSS	Brain Hippocampus Middle	brain
20	chr5:52855800-52857400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr5:52855800-52857400	Active TSS	Colon Smooth Muscle	Colon
22	chr5:52855800-52857400	Active TSS	Fetal Brain Female	brain
23	chr5:52855800-52857400	Active TSS	Fetal Lung	lung
24	chr5:52855800-52857400	Active TSS	A549	lung
25	chr5:52855800-52857600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:52855800-52857600	Active TSS	HMEC	breast
27	chr5:52855800-52857600	Active TSS	K562	blood
28	chr5:52855800-52857800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr5:52855800-52857800	Active TSS	Right Atrium	heart
30	chr5:52855800-52857800	Active TSS	Stomach Smooth Muscle	stomach
31	chr5:52855800-52858000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:52855800-52858200	Active TSS	NHLF	lung
33	chr5:52856000-52856400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr5:52856000-52856400	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr5:52856000-52856400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:52856000-52856400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr5:52856000-52856400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:52856000-52856400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:52856000-52856400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr5:52856000-52856400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr5:52856000-52856800	Active TSS	Primary B cells from cord blood	blood
42	chr5:52856000-52856800	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr5:52856000-52856800	Active TSS	Liver	Liver
44	chr5:52856000-52857000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr5:52856000-52857000	Active TSS	Brain Substantia Nigra	brain
46	chr5:52856000-52857000	Active TSS	Duodenum Mucosa	Duodenum
47	chr5:52856000-52857000	Active TSS	Fetal Kidney	kidney
48	chr5:52856000-52857000	Active TSS	Osteobl	bone
49	chr5:52856000-52857200	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr5:52856000-52857200	Active TSS	Colonic Mucosa	Colon

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