Variant report

Variant	rs62352400
Chromosome Location	chr4:165675108-165675109
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
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	FOXA1	chr4:165674984-165675347	HepG2	liver:	n/a	chr4:165675248-165675263 chr4:165675190-165675205
2	TCF12	chr4:165674941-165675490	A549	lung:	n/a	chr4:165675195-165675204
3	JUND	chr4:165675083-165675462	T-47D	breast:	n/a	n/a
4	FOXA1	chr4:165675051-165675479	T-47D	breast:	n/a	chr4:165675248-165675263 chr4:165675190-165675205
5	GATA3	chr4:165675026-165675419	T-47D	breast:	n/a	chr4:165675080-165675091 chr4:165675076-165675084
6	GATA3	chr4:165675001-165675382	T-47D	breast:	n/a	chr4:165675080-165675091 chr4:165675076-165675084
7	FOXA2	chr4:165674931-165675371	A549	lung:	n/a	n/a
8	FOXA1	chr4:165675021-165675332	T-47D	breast:	n/a	chr4:165675248-165675263 chr4:165675190-165675205

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:165675069-165675119	GM19239	blood:	n/a
2	chr4:165675069-165675119	T-47D	breast:	n/a
3	chr4:165675069-165675119	HEEpiC	esophagus:	n/a
4	chr4:165675069-165675119	HNPCEpiC	eye:	n/a
5	chr4:165675069-165675119	HCPEpiC	choroid plexus:	n/a
6	chr4:165675069-165675119	HCM	heart:	n/a
7	chr4:165675069-165675119	HMEC	breast:	n/a
8	chr4:165675069-165675119	Jurkat	blood:	n/a
9	chr4:165675069-165675119	NT2-D1	testis:	n/a
10	chr4:165675069-165675119	Caco-2	colon:	n/a
11	chr4:165675069-165675119	NHBE	bronchial:	n/a
12	chr4:165675069-165675119	Hela-S3	cervix:	n/a
13	chr4:165675069-165675119	IMR90	lung:	fetal
14	chr4:165675069-165675119	HRPEpiC	eye:	n/a
15	chr4:165675069-165675119	LNCaP	prostate:	n/a
16	chr4:165675069-165675119	A549	lung:	n/a
17	chr4:165675069-165675119	HL-60	blood:	n/a
18	chr4:165675069-165675119	HUVEC	blood vessel:	n/a
19	chr4:165675069-165675119	SKMC	muscle:	n/a
20	chr4:165675069-165675119	SAEC	small airway:	n/a
21	chr4:165675069-165675119	SK-N-MC	brain:	n/a
22	chr4:165675069-165675119	U87	brain:	n/a
23	chr4:165675069-165675119	HRE	kidney:	n/a
24	chr4:165675069-165675119	SK-N-SH	brain:	n/a
25	chr4:165675069-165675119	K562	blood:	n/a
26	chr4:165675069-165675119	AoSMC	blood vessel:	n/a
27	chr4:165675069-165675119	ProgFib	skin:	n/a
28	chr4:165675069-165675119	HAEpiC	amniotic membrane:	n/a
29	chr4:165675069-165675119	HIPEpiC	eye:	n/a
30	chr4:165675069-165675119	NB4	blood:	n/a
31	chr4:165675069-165675119	BE2_C	brain:	n/a
32	chr4:165675069-165675119	HCT-116	colon:	n/a
33	chr4:165675069-165675119	NH-A	brain:	n/a
34	chr4:165675069-165675119	SK-N-SH_RA	brain:	n/a
35	chr4:165675069-165675119	HPAEpiC	pulmonary alveolar:	n/a
36	chr4:165675069-165675119	BJ	skin:	n/a
37	chr4:165675069-165675119	HRCEpiC	kidney:	n/a
38	chr4:165675069-165675119	CMK	blood:	n/a
39	chr4:165675069-165675119	GM12891	blood:	n/a
40	chr4:165675069-165675119	GM12878	blood:	n/a
41	chr4:165675069-165675119	ovcar-3	ovarian:	n/a
42	chr4:165675069-165675119	NHDF-neo	bronchial:	n/a
43	chr4:165675069-165675119	HEK293	kidney:	embryo
44	chr4:165675069-165675119	ECC-1	luminal epithelium:	n/a
45	chr4:165675069-165675119	PrEC	prostate:	n/a
46	chr4:165675069-165675119	AG04450	lung:	fetal
47	chr4:165675069-165675119	AG09319	gingival:	n/a
48	chr4:165675069-165675119	GM06990	blood:	n/a
49	chr4:165675069-165675119	HepG2	liver:	n/a
50	chr4:165675069-165675119	MCF-7	breast:	n/a

No data

Variant related genes	Relation type
ENSG00000248771	TF binding region
ENSG00000248771	CpG island

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10009649	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020055	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025404	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10517823	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435658	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045449	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045455	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045471	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17678924	0.80[ASN][1000 genomes]
rs28373185	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378432	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28387034	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28396291	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28414756	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452058	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28526850	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638469	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28708774	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28715383	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28753124	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28763310	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28799672	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28809627	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28842580	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28871390	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3197940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331736	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337694	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59148630	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352393	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62352396	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352398	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62352401	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352403	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352404	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62352406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62352407	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62352408	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62352409	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352410	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352411	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352412	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352413	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352415	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352416	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352417	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352418	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352419	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352420	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73871394	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73871399	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73871401	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461821	chr4:165402309-165859951	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv596037	chr4:165402309-165859951	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv461822	chr4:165531034-165775547	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv596039	chr4:165531034-165775547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830139	chr4:165619199-165789066	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv10604	chr4:165653826-165724327	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3387225	chr4:165657396-165684323	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	nsv881341	chr4:165661477-165721118	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv881609	chr4:165664864-165721118	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv596040	chr4:165669160-165706611	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv880428	chr4:165669160-165736388	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165673400-165687000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:165674400-165675200	Enhancers	Colonic Mucosa	Colon
3	chr4:165674800-165676400	Active TSS	Fetal Intestine Small	intestine
4	chr4:165674800-165677200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr4:165674800-165678200	Active TSS	Duodenum Mucosa	Duodenum
6	chr4:165674800-165678200	Active TSS	Rectal Mucosa Donor 31	rectum

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