Variant report

Variant	rs62359375
Chromosome Location	chr5:52405432-52405433
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	TCF12	chr5:52405135-52406035	A549	lung:	n/a	n/a
2	YY1	chr5:52405416-52405944	GM12878	blood:	n/a	chr5:52405650-52405661 chr5:52405597-52405611
3	ZMIZ1	chr5:52405376-52405903	K562	blood:	n/a	n/a
4	POLR2A	chr5:52405204-52406024	GM12878	blood:	n/a	n/a
5	SMC3	chr5:52405273-52405471	GM12878	blood:	n/a	n/a
6	E2F6	chr5:52405260-52406043	A549	lung:	n/a	chr5:52405598-52405607 chr5:52405594-52405601 chr5:52405466-52405477 chr5:52405475-52405487 chr5:52405621-52405630
7	POLR2A	chr5:52405275-52406034	H1-neurons	neurons:	n/a	n/a
8	TAF1	chr5:52405403-52405776	GM12891	blood:	n/a	n/a
9	SMC3	chr5:52404785-52405916	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:52405349-52405896	K562	blood:	n/a	n/a
11	TAF1	chr5:52405144-52405974	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr5:52405419-52405849	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr5:52405136-52405980	K562	blood:	n/a	n/a
14	TAF1	chr5:52405236-52405930	GM12892	blood:	n/a	n/a
15	POLR2A	chr5:52405156-52405989	GM19099	blood:	n/a	n/a
16	TAF1	chr5:52405397-52405984	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr5:52405022-52406119	K562	blood:	n/a	n/a
18	POLR2A	chr5:52404785-52405995	K562	blood:	n/a	n/a
19	POLR2A	chr5:52405156-52406077	U87	brain:	n/a	n/a
20	CTCF	chr5:52405420-52405570	HepG2	liver:	n/a	n/a
21	POLR2A	chr5:52404973-52406398	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:52405250-52405998	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr5:52405340-52405921	HepG2	liver:	n/a	n/a
24	ETS1	chr5:52405345-52405883	A549	lung:	n/a	n/a
25	TAF1	chr5:52405398-52406053	MCF-7	breast:	n/a	n/a
26	POU2F2	chr5:52405350-52405964	GM12891	blood:	n/a	n/a
27	POLR2A	chr5:52405345-52406038	HL-60	blood:	n/a	n/a
28	SIN3AK20	chr5:52405220-52405615	HepG2	liver:	n/a	n/a
29	MAX	chr5:52405231-52406052	ECC-1	luminal epithelium:	n/a	chr5:52405647-52405657
30	EGR1	chr5:52405260-52405760	GM12878	blood:	n/a	chr5:52405648-52405658 chr5:52405598-52405607
31	TBP	chr5:52404911-52405998	Hela-S3	cervix:	n/a	n/a
32	REST	chr5:52405294-52405775	SK-N-SH	brain:	n/a	n/a
33	SIN3AK20	chr5:52405312-52406076	MCF-7	breast:	n/a	n/a
34	POLR2A	chr5:52405293-52406304	PBDE	blood:	n/a	n/a
35	POLR2A	chr5:52404781-52405999	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr5:52405296-52405978	K562	blood:	n/a	n/a
37	POLR2A	chr5:52405192-52406039	GM12878	blood:	n/a	n/a
38	BRCA1	chr5:52405412-52405935	Hela-S3	cervix:	n/a	n/a
39	NRF1	chr5:52405298-52405875	GM12878	blood:	n/a	chr5:52405596-52405607 chr5:52405597-52405611 chr5:52405620-52405631 chr5:52405597-52405608 chr5:52405649-52405658 chr5:52405667-52405678 chr5:52405650-52405661
40	MAFK	chr5:52404851-52405964	Hela-S3	cervix:	n/a	n/a
41	MYBL2	chr5:52405380-52406020	HepG2	liver:	n/a	n/a
42	TCF12	chr5:52405416-52405867	GM12878	blood:	n/a	n/a
43	TCF12	chr5:52405209-52405984	ECC-1	luminal epithelium:	n/a	n/a
44	PAX5	chr5:52405241-52406071	GM12878	blood:	n/a	n/a
45	BHLHE40	chr5:52405405-52405919	K562	blood:	n/a	chr5:52405645-52405661
46	E2F6	chr5:52405391-52405806	H1-hESC	embryonic stem cell:	n/a	chr5:52405598-52405607 chr5:52405594-52405601 chr5:52405466-52405477 chr5:52405475-52405487 chr5:52405621-52405630
47	SIN3AK20	chr5:52405141-52405938	K562	blood:	n/a	n/a
48	RCOR1	chr5:52404849-52405906	K562	blood:	n/a	n/a
49	MAX	chr5:52405215-52406083	HepG2	liver:	n/a	chr5:52405647-52405657
50	POLR2A	chr5:52405387-52406039	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
2	chr17:58469116..58469940-chr5:52405166..52406062,2	MCF-7	breast:
3	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:
4	chr5:52405264..52406002-chr6:26204662..26205210,2	HCT-116	colon:
5	chr5:52405061..52405947-chr9:131445854..131446584,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000247796	TF binding region
MOCS2	TF binding region
ENSG00000198518	Chromatin interaction
ENSG00000272123	Chromatin interaction
ENSG00000119335	Chromatin interaction
ENSG00000141371	Chromatin interaction
ENSG00000170832	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12515434	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518145	1.00[ASN][1000 genomes]
rs16880875	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2233209	0.95[EUR][1000 genomes]
rs3212488	1.00[ASN][1000 genomes]
rs3212623	0.82[EUR][1000 genomes]
rs3212632	0.93[EUR][1000 genomes]
rs62359376	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv442948	chr5:52404519-52409439	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr5:52403800-52406600	Active TSS	K562	blood
2	chr5:52404000-52406200	Active TSS	NHLF	lung
3	chr5:52404200-52406000	Active TSS	NHEK	skin
4	chr5:52404400-52405600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:52404400-52406400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52404400-52406400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:52404400-52406400	Active TSS	Psoas Muscle	Psoas
8	chr5:52404400-52406400	Active TSS	GM12878-XiMat	blood
9	chr5:52404600-52406000	Active TSS	Fetal Stomach	stomach
10	chr5:52404600-52406000	Active TSS	Stomach Smooth Muscle	stomach
11	chr5:52404600-52406000	Active TSS	HMEC	breast
12	chr5:52404600-52406200	Active TSS	Brain Hippocampus Middle	brain
13	chr5:52404600-52406200	Active TSS	Colon Smooth Muscle	Colon
14	chr5:52404600-52406200	Active TSS	Fetal Intestine Large	intestine
15	chr5:52404600-52406400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:52404600-52406400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr5:52404600-52406400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:52404600-52406400	Active TSS	Brain Anterior Caudate	brain
19	chr5:52404600-52406600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:52404600-52406600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:52404600-52406600	Active TSS	A549	lung
22	chr5:52404600-52406600	Active TSS	HepG2	liver
23	chr5:52404600-52406600	Active TSS	NHDF-Ad	bronchial
24	chr5:52404600-52407000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr5:52404800-52405800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:52404800-52405800	Active TSS	Primary T cells fromperipheralblood	blood
27	chr5:52404800-52405800	Active TSS	Liver	Liver
28	chr5:52404800-52405800	Active TSS	Fetal Muscle Trunk	muscle
29	chr5:52404800-52405800	Active TSS	Placenta	Placenta
30	chr5:52404800-52406000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:52404800-52406000	Active TSS	Colonic Mucosa	Colon
32	chr5:52404800-52406000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr5:52404800-52406000	Active TSS	Fetal Muscle Leg	muscle
34	chr5:52404800-52406000	Active TSS	Thymus	Thymus
35	chr5:52404800-52406200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr5:52404800-52406200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr5:52404800-52406200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:52404800-52406200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:52404800-52406200	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr5:52404800-52406200	Active TSS	Aorta	Aorta
41	chr5:52404800-52406200	Active TSS	Esophagus	oesophagus
42	chr5:52404800-52406200	Active TSS	Fetal Kidney	kidney
43	chr5:52404800-52406200	Active TSS	Fetal Thymus	thymus
44	chr5:52404800-52406200	Active TSS	Rectal Smooth Muscle	rectum
45	chr5:52404800-52406400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:52404800-52406400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr5:52404800-52406400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:52404800-52406400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr5:52404800-52406400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:52404800-52406400	Active TSS	Duodenum Smooth Muscle	Duodenum

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