Variant report

Variant	rs73754255
Chromosome Location	chr5:52856487-52856488
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	MYC	chr5:52856398-52856566	HUVEC	blood vessel:	n/a	n/a
3	REST	chr5:52856014-52857419	H1-neurons	neurons:	n/a	n/a
4	CEBPB	chr5:52856056-52856712	ECC-1	luminal epithelium:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
5	TAF1	chr5:52856294-52856924	K562	blood:	n/a	n/a
6	YY1	chr5:52856241-52857042	GM12878	blood:	n/a	chr5:52856629-52856641 chr5:52856630-52856640 chr5:52856482-52856502
7	GTF2F1	chr5:52856116-52857111	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr5:52856012-52856944	A549	lung:	n/a	n/a
9	GATA1	chr5:52856000-52857064	PBDE	blood:	n/a	n/a
10	POLR2A	chr5:52856295-52856831	K562	blood:	n/a	n/a
11	CEBPB	chr5:52856207-52856674	HepG2	liver:	n/a	chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
12	POLR2A	chr5:52856304-52857057	Raji	blood:	n/a	n/a
13	CTCF	chr5:52856400-52856550	AG04449	skin:	n/a	n/a
14	POLR2A	chr5:52856315-52857005	GM12892	blood:	n/a	n/a
15	CEBPD	chr5:52856349-52856673	HepG2	liver:	n/a	chr5:52856397-52856408 chr5:52856398-52856407
16	POLR2A	chr5:52856159-52857059	GM12892	blood:	n/a	n/a
17	CEBPB	chr5:52856168-52856539	K562	blood:	n/a	chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
18	POLR2A	chr5:52856380-52856959	GM12878	blood:	n/a	n/a
19	CTCF	chr5:52856480-52856630	HPAF	blood vessel:	n/a	n/a
20	BCLAF1	chr5:52856204-52856955	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:52856380-52856697	HUVEC	blood vessel:	n/a	n/a
22	RCOR1	chr5:52856307-52857050	K562	blood:	n/a	n/a
23	TAF1	chr5:52856257-52856724	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr5:52856355-52856990	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPD	chr5:52856263-52856582	HepG2	liver:	n/a	chr5:52856397-52856408 chr5:52856398-52856407
26	SIN3A	chr5:52856281-52857124	H1-hESC	embryonic stem cell:	n/a	n/a
27	CBX3	chr5:52856124-52856812	HCT-116	colon:	n/a	n/a
28	TBP	chr5:52856026-52857044	K562	blood:	n/a	n/a
29	POLR2A	chr5:52856313-52856927	IMR90	lung:	n/a	n/a
30	TCF7L2	chr5:52856335-52856694	PANC-1	pancreas:	n/a	n/a
31	TCF12	chr5:52856381-52856561	H1-hESC	embryonic stem cell:	n/a	n/a
32	TBL1XR1	chr5:52856196-52857073	K562	blood:	n/a	n/a
33	TAF1	chr5:52856337-52856874	HepG2	liver:	n/a	n/a
34	TAF1	chr5:52856362-52856938	GM12891	blood:	n/a	n/a
35	POLR2A	chr5:52856312-52857024	K562	blood:	n/a	n/a
36	CEBPB	chr5:52855992-52856940	MCF-7	breast:	n/a	chr5:52856074-52856086 chr5:52856396-52856409 chr5:52856396-52856409 chr5:52856398-52856407
37	POLR2A	chr5:52856099-52857076	PFSK-1	brain:	n/a	n/a
38	EP300	chr5:52856119-52857039	K562	blood:	n/a	chr5:52856374-52856388
39	POLR2A	chr5:52856312-52857039	GM12891	blood:	n/a	n/a
40	YY1	chr5:52856286-52856978	GM12878	blood:	n/a	chr5:52856629-52856641 chr5:52856630-52856640 chr5:52856482-52856502
41	BCLAF1	chr5:52856317-52856950	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr5:52856331-52856729	A549	lung:	n/a	n/a
43	PML	chr5:52856235-52856948	K562	blood:	n/a	n/a
44	FOXA1	chr5:52856353-52856809	T-47D	breast:	n/a	n/a
45	STAT3	chr5:52856236-52856575	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr5:52856311-52857089	GM19099	blood:	n/a	n/a
47	POLR2A	chr5:52856376-52856583	A549	lung:	n/a	n/a
48	CHD2	chr5:52856363-52856944	K562	blood:	n/a	n/a
49	ELF1	chr5:52856222-52856646	A549	lung:	n/a	n/a
50	MYC	chr5:52856358-52856779	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:52856452-52856502	HUVEC	blood vessel:	n/a
2	chr5:52856460-52856510	Jurkat	blood:	n/a
3	chr5:52856452-52856502	MCF10A-Er-Src	breast:	n/a
4	chr5:52856476-52856526	SK-N-SH_RA	brain:	n/a
5	chr5:52856452-52856502	PrEC	prostate:	n/a
6	chr5:52856460-52856510	HUVEC	blood vessel:	n/a
7	chr5:52856460-52856510	ovcar-3	ovarian:	n/a
8	chr5:52856460-52856510	HRCEpiC	kidney:	n/a
9	chr5:52856460-52856510	BE2_C	brain:	n/a
10	chr5:52856460-52856510	HPAEpiC	pulmonary alveolar:	n/a
11	chr5:52856476-52856526	PFSK-1	brain:	n/a
12	chr5:52856460-52856510	NHBE	bronchial:	n/a
13	chr5:52856476-52856526	Jurkat	blood:	n/a
14	chr5:52856460-52856510	ProgFib	skin:	n/a
15	chr5:52856476-52856526	HNPCEpiC	eye:	n/a
16	chr5:52856460-52856510	Hela-S3	cervix:	n/a
17	chr5:52856476-52856526	GM12891	blood:	n/a
18	chr5:52856476-52856526	AG10803	skin:	n/a
19	chr5:52856476-52856526	NB4	blood:	n/a
20	chr5:52856476-52856526	MCF-7	breast:	n/a
21	chr5:52856452-52856502	HEK293	kidney:	embryo
22	chr5:52856452-52856502	AG09309	skin:	n/a
23	chr5:52856452-52856502	HEEpiC	esophagus:	n/a
24	chr5:52856476-52856526	AG09309	skin:	n/a
25	chr5:52856460-52856510	SAEC	small airway:	n/a
26	chr5:52856452-52856502	BJ	skin:	n/a
27	chr5:52856476-52856526	HIPEpiC	eye:	n/a
28	chr5:52856452-52856502	GM19239	blood:	n/a
29	chr5:52856460-52856510	HIPEpiC	eye:	n/a
30	chr5:52856452-52856502	HCT-116	colon:	n/a
31	chr5:52856476-52856526	AoSMC	blood vessel:	n/a
32	chr5:52856460-52856510	GM12892	blood:	n/a
33	chr5:52856476-52856526	H1-hESC	embryonic stem cell:	embryo
34	chr5:52856476-52856526	HEEpiC	esophagus:	n/a
35	chr5:52856452-52856502	HepG2	liver:	n/a
36	chr5:52856460-52856510	SK-N-MC	brain:	n/a
37	chr5:52856476-52856526	HCM	heart:	n/a
38	chr5:52856476-52856526	HMEC	breast:	n/a
39	chr5:52856476-52856526	SK-N-SH	brain:	n/a
40	chr5:52856452-52856502	ProgFib	skin:	n/a
41	chr5:52856452-52856502	Hepatocyte	liver:	n/a
42	chr5:52856476-52856526	HRPEpiC	eye:	n/a
43	chr5:52856452-52856502	AoSMC	blood vessel:	n/a
44	chr5:52856476-52856526	HEK293	kidney:	embryo
45	chr5:52856460-52856510	HL-60	blood:	n/a
46	chr5:52856460-52856510	GM19239	blood:	n/a
47	chr5:52856460-52856510	HNPCEpiC	eye:	n/a
48	chr5:52856452-52856502	HCPEpiC	choroid plexus:	n/a
49	chr5:52856476-52856526	HRCEpiC	kidney:	n/a
50	chr5:52856460-52856510	SK-N-SH_RA	brain:	n/a

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
NDUFS4	CpG island
ENSG00000267898	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs56069975	1.00[AFR][1000 genomes]
rs56682747	1.00[AFR][1000 genomes]
rs56848052	1.00[AFR][1000 genomes]
rs57292254	1.00[AFR][1000 genomes]
rs58915856	1.00[AFR][1000 genomes]
rs59431273	1.00[AFR][1000 genomes]
rs60419326	1.00[AFR][1000 genomes]
rs61695021	1.00[AFR][1000 genomes]
rs73754254	1.00[AFR][1000 genomes]
rs73754257	1.00[AFR][1000 genomes]
rs73754258	1.00[AFR][1000 genomes]
rs73754259	0.83[AFR][1000 genomes]
rs73754260	1.00[AFR][1000 genomes]
rs73754266	1.00[AFR][1000 genomes]
rs73754269	1.00[AFR][1000 genomes]
rs73754270	1.00[AFR][1000 genomes]
rs73754272	0.85[AFR][1000 genomes]
rs73754273	1.00[AFR][1000 genomes]
rs73754276	1.00[AFR][1000 genomes]
rs73754277	1.00[AFR][1000 genomes]
rs73754278	1.00[AFR][1000 genomes]
rs73754280	1.00[AFR][1000 genomes]
rs73754283	1.00[AFR][1000 genomes]
rs73754285	1.00[AFR][1000 genomes]
rs73754286	1.00[AFR][1000 genomes]
rs73754287	1.00[AFR][1000 genomes]
rs73754295	1.00[AFR][1000 genomes]
rs73754297	1.00[AFR][1000 genomes]

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:127 , 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	chr5:52855800-52856600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:52855800-52856600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:52855800-52856600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:52855800-52856600	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr5:52855800-52856800	Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr5:52855800-52857000	Active TSS	Primary T cells from cord blood	blood
8	chr5:52855800-52857200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:52855800-52857200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr5:52855800-52857200	Active TSS	Hela-S3	cervix
11	chr5:52855800-52857400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:52855800-52857400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:52855800-52857400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr5:52855800-52857400	Active TSS	Brain Anterior Caudate	brain
15	chr5:52855800-52857400	Active TSS	Brain Cingulate Gyrus	brain
16	chr5:52855800-52857400	Active TSS	Brain Hippocampus Middle	brain
17	chr5:52855800-52857400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr5:52855800-52857400	Active TSS	Colon Smooth Muscle	Colon
19	chr5:52855800-52857400	Active TSS	Fetal Brain Female	brain
20	chr5:52855800-52857400	Active TSS	Fetal Lung	lung
21	chr5:52855800-52857400	Active TSS	A549	lung
22	chr5:52855800-52857600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:52855800-52857600	Active TSS	HMEC	breast
24	chr5:52855800-52857600	Active TSS	K562	blood
25	chr5:52855800-52857800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr5:52855800-52857800	Active TSS	Right Atrium	heart
27	chr5:52855800-52857800	Active TSS	Stomach Smooth Muscle	stomach
28	chr5:52855800-52858000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:52855800-52858200	Active TSS	NHLF	lung
30	chr5:52856000-52856800	Active TSS	Primary B cells from cord blood	blood
31	chr5:52856000-52856800	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr5:52856000-52856800	Active TSS	Liver	Liver
33	chr5:52856000-52857000	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr5:52856000-52857000	Active TSS	Brain Substantia Nigra	brain
35	chr5:52856000-52857000	Active TSS	Duodenum Mucosa	Duodenum
36	chr5:52856000-52857000	Active TSS	Fetal Kidney	kidney
37	chr5:52856000-52857000	Active TSS	Osteobl	bone
38	chr5:52856000-52857200	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr5:52856000-52857200	Active TSS	Colonic Mucosa	Colon
40	chr5:52856000-52857200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr5:52856000-52857200	Active TSS	Placenta	Placenta
42	chr5:52856000-52857200	Active TSS	Rectal Smooth Muscle	rectum
43	chr5:52856000-52857200	Bivalent/Poised TSS	HepG2	liver
44	chr5:52856000-52857400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr5:52856000-52857400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:52856000-52857400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:52856000-52857400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:52856000-52857400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:52856000-52857400	Active TSS	Fetal Heart	heart
50	chr5:52856000-52857400	Active TSS	Fetal Intestine Large	intestine

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