Variant report

Variant	rs55746682
Chromosome Location	chr3:19975497-19975498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr3:19975455-19975861	K562	blood:	n/a	n/a
2	MAZ	chr3:19975092-19975969	K562	blood:	n/a	n/a
3	YY1	chr3:19975282-19976016	H1-hESC	embryonic stem cell:	n/a	chr3:19975696-19975708
4	TAF1	chr3:19975474-19975897	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr3:19975484-19975890	H1-hESC	embryonic stem cell:	n/a	chr3:19975696-19975708
6	CBX3	chr3:19975421-19975955	K562	blood:	n/a	n/a
7	RCOR1	chr3:19975212-19975919	K562	blood:	n/a	n/a
8	YY1	chr3:19975339-19975878	K562	blood:	n/a	chr3:19975696-19975708
9	JUND	chr3:19975326-19975966	K562	blood:	n/a	n/a
10	POLR2A	chr3:19975417-19975994	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr3:19975336-19975961	K562	blood:	n/a	n/a
12	TBP	chr3:19975422-19976094	K562	blood:	n/a	n/a
13	NR2F2	chr3:19975311-19976215	K562	blood:	n/a	n/a
14	RCOR1	chr3:19972538-19976115	K562	blood:	n/a	n/a
15	ZC3H11A	chr3:19975321-19976147	K562	blood:	n/a	n/a
16	UBTF	chr3:19975046-19975949	K562	blood:	n/a	n/a
17	SP1	chr3:19975451-19975798	H1-hESC	embryonic stem cell:	n/a	chr3:19975732-19975744 chr3:19975733-19975743 chr3:19975734-19975743 chr3:19975733-19975742 chr3:19975732-19975744 chr3:19975734-19975743 chr3:19975733-19975743

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:19975483-19975533	LNCaP	prostate:	n/a
2	chr3:19975483-19975533	AG09309	skin:	n/a
3	chr3:19975483-19975533	PrEC	prostate:	n/a
4	chr3:19975483-19975533	MCF10A-Er-Src	breast:	n/a
5	chr3:19975483-19975533	HCF	heart:	n/a
6	chr3:19975483-19975533	ProgFib	skin:	n/a
7	chr3:19975483-19975533	ovcar-3	ovarian:	n/a
8	chr3:19975483-19975533	AG09319	gingival:	n/a
9	chr3:19975483-19975533	Hela-S3	cervix:	n/a
10	chr3:19975483-19975533	ECC-1	luminal epithelium:	n/a
11	chr3:19975483-19975533	HRPEpiC	eye:	n/a
12	chr3:19975483-19975533	NHDF-neo	bronchial:	n/a
13	chr3:19975483-19975533	U87	brain:	n/a
14	chr3:19975483-19975533	SKMC	muscle:	n/a
15	chr3:19975483-19975533	BJ	skin:	n/a
16	chr3:19975483-19975533	HRE	kidney:	n/a
17	chr3:19975483-19975533	HMEC	breast:	n/a
18	chr3:19975483-19975533	HIPEpiC	eye:	n/a
19	chr3:19975483-19975533	RPTEC	kidney:	n/a
20	chr3:19975483-19975533	HEEpiC	esophagus:	n/a
21	chr3:19975483-19975533	HRCEpiC	kidney:	n/a
22	chr3:19975483-19975533	SK-N-SH	brain:	n/a
23	chr3:19975483-19975533	SK-N-SH_RA	brain:	n/a
24	chr3:19975483-19975533	K562	blood:	n/a
25	chr3:19975483-19975533	A549	lung:	n/a
26	chr3:19975483-19975533	H1-hESC	embryonic stem cell:	embryo
27	chr3:19975483-19975533	SK-N-MC	brain:	n/a
28	chr3:19975483-19975533	GM19239	blood:	n/a
29	chr3:19975483-19975533	Caco-2	colon:	n/a
30	chr3:19975483-19975533	HEK293	kidney:	embryo
31	chr3:19975483-19975533	PANC-1	pancreas:	n/a
32	chr3:19975483-19975533	HNPCEpiC	eye:	n/a
33	chr3:19975483-19975533	AG04449	skin:	fetal
34	chr3:19975483-19975533	HepG2	liver:	n/a
35	chr3:19975483-19975533	HCPEpiC	choroid plexus:	n/a
36	chr3:19975483-19975533	GM12891	blood:	n/a
37	chr3:19975483-19975533	MCF-7	breast:	n/a
38	chr3:19975483-19975533	NHBE	bronchial:	n/a
39	chr3:19975483-19975533	HCM	heart:	n/a
40	chr3:19975483-19975533	SAEC	small airway:	n/a
41	chr3:19975483-19975533	AG10803	skin:	n/a
42	chr3:19975483-19975533	AG04450	lung:	fetal
43	chr3:19975483-19975533	NT2-D1	testis:	n/a
44	chr3:19975483-19975533	HUVEC	blood vessel:	n/a
45	chr3:19975483-19975533	Jurkat	blood:	n/a
46	chr3:19975483-19975533	AoSMC	blood vessel:	n/a
47	chr3:19975483-19975533	BE2_C	brain:	n/a
48	chr3:19975483-19975533	HL-60	blood:	n/a
49	chr3:19975483-19975533	CMK	blood:	n/a
50	chr3:19975483-19975533	PFSK-1	brain:	n/a

No data

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

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11924875	1.00[EUR][1000 genomes]
rs11925668	1.00[AMR][1000 genomes]
rs11929340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13317268	1.00[AMR][1000 genomes]
rs13340108	1.00[EUR][1000 genomes]
rs1605195	1.00[EUR][1000 genomes]
rs17006349	1.00[EUR][1000 genomes]
rs2001650	1.00[EUR][1000 genomes]
rs28886381	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55851373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58512353	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58603530	1.00[EUR][1000 genomes]
rs59572420	0.92[AFR][1000 genomes]
rs61068672	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61139478	1.00[EUR][1000 genomes]
rs61152961	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6550130	1.00[EUR][1000 genomes]
rs6550210	1.00[EUR][1000 genomes]
rs6550212	1.00[EUR][1000 genomes]
rs6550216	1.00[EUR][1000 genomes]
rs6791245	1.00[EUR][1000 genomes]
rs6805780	1.00[EUR][1000 genomes]
rs73173912	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73176006	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73176093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73184830	1.00[EUR][1000 genomes]
rs73184831	1.00[EUR][1000 genomes]
rs73184832	1.00[EUR][1000 genomes]
rs73184839	1.00[EUR][1000 genomes]
rs73184842	1.00[EUR][1000 genomes]
rs73188422	1.00[AMR][1000 genomes]
rs73190456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73190462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624970	1.00[EUR][1000 genomes]
rs7629079	1.00[EUR][1000 genomes]
rs7651609	1.00[EUR][1000 genomes]
rs9834480	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840739	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9847647	1.00[EUR][1000 genomes]
rs9850421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850795	1.00[AMR][1000 genomes]
rs9854666	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861798	1.00[EUR][1000 genomes]
rs9869783	1.00[AMR][1000 genomes]
rs9875453	1.00[AMR][1000 genomes]
rs9881822	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19973600-19979200	Weak transcription	HMEC	breast
2	chr3:19973600-19987200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:19973800-19978400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:19973800-19979000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:19974200-19979200	Weak transcription	Hela-S3	cervix
6	chr3:19974600-19976000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:19974800-19975800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:19975000-19975600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:19975000-19976000	Enhancers	HepG2	liver
10	chr3:19975000-19976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:19975200-19976000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:19975200-19976000	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr3:19975200-19976000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:19975200-19976400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:19975200-19976400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:19975400-19975600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:19975400-19975800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:19975400-19975800	Enhancers	Psoas Muscle	Psoas
19	chr3:19975400-19976000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:19975400-19976000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:19975400-19976000	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr3:19975400-19976000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:19975400-19976000	Flanking Active TSS	K562	blood
24	chr3:19975400-19976200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:19975400-19976200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr3:19975400-19976200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:19975400-19976200	Enhancers	A549	lung

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