Variant report

Variant	rs62392212
Chromosome Location	chr5:177581346-177581347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr5:177580776-177581352	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr5:177576695-177581508	MCF-7	breast:	n/a	n/a
3	CEBPB	chr5:177580776-177581517	A549	lung:	n/a	chr5:177581467-177581478 chr5:177581467-177581480 chr5:177581469-177581480
4	RFX5	chr5:177580188-177581828	SK-N-SH	brain:	n/a	chr5:177580925-177580934
5	ZNF384	chr5:177580789-177581362	K562	blood:	n/a	n/a
6	POLR2A	chr5:177572629-177581352	GM12891	blood:	n/a	n/a
7	NR2F2	chr5:177580657-177581644	K562	blood:	n/a	n/a
8	CEBPB	chr5:177580697-177581401	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:177579628-177581491	HepG2	liver:	n/a	n/a
10	MXI1	chr5:177579342-177581543	SK-N-SH	brain:	n/a	n/a
11	GABPA	chr5:177579997-177581878	MCF-7	breast:	n/a	n/a
12	MYBL2	chr5:177580680-177581629	HepG2	liver:	n/a	n/a
13	CEBPB	chr5:177580894-177581476	K562	blood:	n/a	n/a
14	POLR2A	chr5:177580071-177584361	K562	blood:	n/a	n/a
15	POLR2A	chr5:177580673-177581734	HepG2	liver:	n/a	n/a
16	POLR2A	chr5:177579609-177581367	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:177580259-177581366	HUVEC	blood vessel:	n/a	n/a
18	MAZ	chr5:177580828-177581476	HepG2	liver:	n/a	chr5:177581120-177581130
19	CEBPB	chr5:177580732-177581363	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:177572824-177581372	K562	blood:	n/a	n/a
21	STAT3	chr5:177580800-177581389	MCF10A-Er-Src	breast:	n/a	chr5:177580938-177580945
22	CEBPB	chr5:177580836-177581649	HepG2	liver:	n/a	chr5:177581467-177581478 chr5:177581467-177581480 chr5:177581469-177581480
23	POLR2A	chr5:177580552-177581364	SK-N-SH	brain:	n/a	n/a
24	MAX	chr5:177579558-177581351	MCF-7	breast:	n/a	chr5:177581120-177581130
25	MAX	chr5:177580673-177581744	HepG2	liver:	n/a	chr5:177581120-177581130
26	POLR2A	chr5:177580281-177581461	SK-N-MC	brain:	n/a	n/a
27	CEBPB	chr5:177580832-177581375	IMR90	lung:	n/a	n/a
28	CEBPB	chr5:177580901-177581668	HepG2	liver:	n/a	chr5:177581467-177581478 chr5:177581467-177581480 chr5:177581469-177581480
29	NRF1	chr5:177580415-177581410	SK-N-SH	brain:	n/a	n/a
30	CEBPB	chr5:177580758-177581367	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:177581310-177581360	AG10803	skin:	n/a
2	chr5:177581310-177581360	HepG2	liver:	n/a
3	chr5:177581310-177581360	HCF	heart:	n/a
4	chr5:177581310-177581360	LNCaP	prostate:	n/a
5	chr5:177581310-177581360	HRCEpiC	kidney:	n/a
6	chr5:177581310-177581360	K562	blood:	n/a
7	chr5:177581310-177581360	GM12878	blood:	n/a
8	chr5:177581310-177581360	HCT-116	colon:	n/a
9	chr5:177581310-177581360	A549	lung:	n/a
10	chr5:177581310-177581360	ECC-1	luminal epithelium:	n/a
11	chr5:177581310-177581360	HMEC	breast:	n/a
12	chr5:177581310-177581360	SKMC	muscle:	n/a
13	chr5:177581310-177581360	AG04449	skin:	fetal
14	chr5:177581310-177581360	PANC-1	pancreas:	n/a
15	chr5:177581310-177581360	HNPCEpiC	eye:	n/a
16	chr5:177581310-177581360	NB4	blood:	n/a
17	chr5:177581310-177581360	PFSK-1	brain:	n/a
18	chr5:177581310-177581360	Hela-S3	cervix:	n/a
19	chr5:177581310-177581360	U87	brain:	n/a
20	chr5:177581310-177581360	ovcar-3	ovarian:	n/a
21	chr5:177581310-177581360	HIPEpiC	eye:	n/a
22	chr5:177581310-177581360	SK-N-SH_RA	brain:	n/a
23	chr5:177581310-177581360	PrEC	prostate:	n/a
24	chr5:177581310-177581360	HPAEpiC	pulmonary alveolar:	n/a
25	chr5:177581310-177581360	T-47D	breast:	n/a
26	chr5:177581310-177581360	GM12891	blood:	n/a
27	chr5:177581310-177581360	IMR90	lung:	fetal
28	chr5:177581310-177581360	BE2_C	brain:	n/a
29	chr5:177581310-177581360	GM06990	blood:	n/a
30	chr5:177581310-177581360	HUVEC	blood vessel:	n/a
31	chr5:177581310-177581360	NH-A	brain:	n/a
32	chr5:177581310-177581360	H1-hESC	embryonic stem cell:	embryo
33	chr5:177581310-177581360	Hepatocyte	liver:	n/a
34	chr5:177581310-177581360	AG09309	skin:	n/a
35	chr5:177581310-177581360	MCF10A-Er-Src	breast:	n/a
36	chr5:177581310-177581360	ProgFib	skin:	n/a
37	chr5:177581310-177581360	HAEpiC	amniotic membrane:	n/a
38	chr5:177581310-177581360	HEK293	kidney:	embryo
39	chr5:177581310-177581360	GM19239	blood:	n/a
40	chr5:177581310-177581360	HCM	heart:	n/a
41	chr5:177581310-177581360	AG04450	lung:	fetal
42	chr5:177581310-177581360	SK-N-MC	brain:	n/a
43	chr5:177581310-177581360	HEEpiC	esophagus:	n/a
44	chr5:177581310-177581360	RPTEC	kidney:	n/a
45	chr5:177581310-177581360	NHDF-neo	bronchial:	n/a
46	chr5:177581310-177581360	HRE	kidney:	n/a
47	chr5:177581310-177581360	Caco-2	colon:	n/a
48	chr5:177581310-177581360	HL-60	blood:	n/a
49	chr5:177581310-177581360	SAEC	small airway:	n/a
50	chr5:177581310-177581360	CMK	blood:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177539791..177542194-chr5:177578689..177582162,4	K562	blood:
2	chr5:177539043..177545979-chr5:177577141..177584026,12	K562	blood:
3	chr5:177579578..177582486-chr5:177629664..177632966,4	K562	blood:
4	chr5:177556550..177559096-chr5:177579482..177582645,4	K562	blood:
5	chr5:177580997..177581515-chr5:177590843..177591430,2	K562	blood:
6	chr5:177579489..177582257-chr5:177628656..177632410,3	K562	blood:
7	chr5:177556214..177559808-chr5:177575521..177582645,10	K562	blood:
8	chr5:177578478..177582579-chr5:177629428..177633237,12	MCF-7	breast:
9	chr5:177501753..177504683-chr5:177581029..177582623,2	K562	blood:

No data

Variant related genes	Relation type
NHP2	TF binding region
NHP2	CpG island
ENSG00000145911	Chromatin interaction
ENSG00000145916	Chromatin interaction
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10042021	0.83[ASN][1000 genomes]
rs11952173	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11956103	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13183880	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13184023	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13185017	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13189047	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34594900	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35885458	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4549545	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601220	0.87[ASN][1000 genomes]
rs6601222	0.89[ASN][1000 genomes]
rs66486976	0.85[ASN][1000 genomes]
rs6870391	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6878464	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6878624	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6893797	0.87[ASN][1000 genomes]
rs7379278	0.84[ASN][1000 genomes]
rs7380934	0.81[ASN][1000 genomes]
rs7710186	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7732415	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
4	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
5	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1017664	chr5:177578194-177633116	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
8	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177579400-177581400	Active TSS	HSMM	muscle
2	chr5:177579800-177581400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr5:177579800-177581400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:177579800-177581400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:177579800-177581400	Active TSS	Fetal Kidney	kidney
6	chr5:177579800-177581800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:177580000-177581400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:177580000-177581400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:177580000-177581400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr5:177580000-177581400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr5:177580000-177581400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr5:177580000-177581400	Active TSS	Psoas Muscle	Psoas
13	chr5:177580000-177581400	Active TSS	A549	lung
14	chr5:177580000-177581800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr5:177580200-177581400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:177580200-177581400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:177580200-177581400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:177580200-177581400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:177580200-177581400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:177580200-177581400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:177580200-177581400	Active TSS	Muscle Satellite Cultured Cells	--
22	chr5:177580200-177581400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:177580200-177581400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:177580200-177581400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:177580200-177581400	Active TSS	Esophagus	oesophagus
26	chr5:177580200-177581400	Active TSS	Gastric	stomach
27	chr5:177580200-177581400	Active TSS	Left Ventricle	heart
28	chr5:177580200-177581400	Active TSS	Ovary	ovary
29	chr5:177580200-177581400	Active TSS	Right Atrium	heart
30	chr5:177580200-177581400	Active TSS	Right Ventricle	heart
31	chr5:177580200-177581400	Active TSS	HMEC	breast
32	chr5:177580200-177581400	Active TSS	K562	blood
33	chr5:177580200-177581600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr5:177580200-177581600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr5:177580200-177581800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:177580200-177581800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:177580400-177581400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:177580400-177581400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:177580400-177581400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:177580400-177581400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr5:177580400-177581400	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr5:177580400-177581400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:177580400-177581400	Active TSS	Brain Hippocampus Middle	brain
44	chr5:177580400-177581400	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr5:177580400-177581400	Active TSS	Brain Substantia Nigra	brain
46	chr5:177580400-177581400	Active TSS	Fetal Lung	lung
47	chr5:177580400-177581400	Active TSS	Placenta	Placenta
48	chr5:177580400-177581400	Active TSS	Fetal Stomach	stomach
49	chr5:177580400-177581400	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr5:177580400-177581400	Active TSS	HUVEC	blood vessel

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