Variant report

Variant	rs7654237
Chromosome Location	chr4:124671501-124671502
allele	C/G
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	MAX	chr4:124670870-124671838	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr4:124670936-124671800	ECC-1	luminal epithelium:	n/a	n/a
3	SMC3	chr4:124671233-124671646	Hela-S3	cervix:	n/a	n/a
4	ZNF143	chr4:124671158-124671705	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOXA1	chr4:124671195-124671667	HepG2	liver:	n/a	n/a
6	TEAD4	chr4:124670981-124671773	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr4:124670769-124671979	ECC-1	luminal epithelium:	n/a	n/a
8	TCF7L2	chr4:124671147-124671576	Hela-S3	cervix:	n/a	n/a
9	ESR1	chr4:124671031-124671697	ECC-1	luminal epithelium:	n/a	n/a
10	FOXA2	chr4:124671338-124671615	HepG2	liver:	n/a	n/a
11	SPI1	chr4:124671091-124671559	HL-60	blood:	n/a	chr4:124671301-124671314 chr4:124671302-124671315 chr4:124671157-124671170
12	POLR2A	chr4:124671151-124671671	ECC-1	luminal epithelium:	n/a	n/a
13	RCOR1	chr4:124671201-124671586	Hela-S3	cervix:	n/a	n/a
14	FOXM1	chr4:124670430-124671893	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr4:124671292-124671615	Hela-S3	cervix:	n/a	chr4:124671303-124671312
16	KAP1	chr4:124670984-124671756	HEK293	kidney:	n/a	n/a
17	FOXA1	chr4:124671242-124671678	ECC-1	luminal epithelium:	n/a	n/a
18	ESR1	chr4:124671050-124671660	ECC-1	luminal epithelium:	n/a	n/a
19	RAD21	chr4:124671156-124671659	Hela-S3	cervix:	n/a	n/a
20	HNF4A	chr4:124671235-124671556	HepG2	liver:	n/a	chr4:124671419-124671434 chr4:124671419-124671434 chr4:124671421-124671433 chr4:124671420-124671428 chr4:124671420-124671434
21	TCF7L2	chr4:124671159-124671612	HCT-116	colon:	n/a	n/a
22	TEAD4	chr4:124671118-124671533	H1-hESC	embryonic stem cell:	n/a	n/a
23	ESR1	chr4:124671076-124671611	ECC-1	luminal epithelium:	n/a	n/a
24	RAD21	chr4:124670979-124671814	ECC-1	luminal epithelium:	n/a	n/a
25	ESR1	chr4:124671065-124671680	ECC-1	luminal epithelium:	n/a	n/a
26	FOXM1	chr4:124670970-124671861	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr4:124671379-124671521	HepG2	liver:	n/a	n/a
28	EP300	chr4:124671275-124671695	HepG2	liver:	n/a	chr4:124671303-124671312
29	NFIC	chr4:124670786-124671776	ECC-1	luminal epithelium:	n/a	n/a
30	ESR1	chr4:124671096-124671649	ECC-1	luminal epithelium:	n/a	n/a
31	CEBPB	chr4:124671143-124671513	ECC-1	luminal epithelium:	n/a	n/a
32	TCF12	chr4:124670543-124671940	ECC-1	luminal epithelium:	n/a	n/a
33	TEAD4	chr4:124671201-124671724	HepG2	liver:	n/a	n/a
34	CEBPB	chr4:124671124-124671726	ECC-1	luminal epithelium:	n/a	n/a
35	NR3C1	chr4:124671167-124671585	ECC-1	luminal epithelium:	n/a	n/a
36	KAP1	chr4:124670994-124671665	U2OS	brain:	n/a	n/a
37	YY1	chr4:124671042-124671620	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr4:124671086-124671967	ECC-1	luminal epithelium:	n/a	n/a
39	MAX	chr4:124671191-124671642	Hela-S3	cervix:	n/a	n/a
40	FOXA1	chr4:124671330-124671630	ECC-1	luminal epithelium:	n/a	n/a
41	USF2	chr4:124671221-124671561	Hela-S3	cervix:	n/a	n/a
42	RAD21	chr4:124671112-124671674	ECC-1	luminal epithelium:	n/a	n/a
43	EP300	chr4:124671195-124671639	HepG2	liver:	n/a	chr4:124671303-124671312
44	HDAC2	chr4:124671218-124671573	HepG2	liver:	n/a	n/a
45	TEAD4	chr4:124670835-124671804	ECC-1	luminal epithelium:	n/a	n/a
46	HNF4G	chr4:124671224-124671575	HepG2	liver:	n/a	chr4:124671420-124671435 chr4:124671419-124671434 chr4:124671421-124671433 chr4:124671420-124671428 chr4:124671420-124671434
47	ARID3A	chr4:124671323-124671561	HepG2	liver:	n/a	n/a
48	ESR1	chr4:124671182-124671648	ECC-1	luminal epithelium:	n/a	n/a
49	NR3C1	chr4:124671084-124671677	ECC-1	luminal epithelium:	n/a	n/a
50	EP300	chr4:124670942-124671823	ECC-1	luminal epithelium:	n/a	chr4:124670958-124670967 chr4:124670954-124670968 chr4:124671303-124671312

Variant related genes	Relation type
RPL21P50	TF binding region
ENSG00000226655	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11725042	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735598	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12641914	0.85[ASN][1000 genomes]
rs12642158	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12646820	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13121568	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13129313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13147789	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1433218	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2390584	0.87[ASN][1000 genomes]
rs3097913	1.00[CEU][hapmap]
rs3097925	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3097926	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113362	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3113363	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113364	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3113366	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3113367	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3113380	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3113385	1.00[CEU][hapmap]
rs3113386	0.85[EUR][1000 genomes]
rs34360247	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34796024	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35981807	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36061481	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62321771	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62321800	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6840618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6855549	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs721456	1.00[CEU][hapmap]
rs7699221	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124663600-124676600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:124667200-124676200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:124667400-124673200	Weak transcription	Aorta	Aorta
4	chr4:124667800-124672000	Enhancers	Fetal Muscle Leg	muscle
5	chr4:124668200-124671800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr4:124668200-124671800	Enhancers	Fetal Heart	heart
7	chr4:124670000-124671600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:124670000-124671800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:124670000-124671800	Enhancers	Fetal Lung	lung
10	chr4:124670000-124672200	Enhancers	Fetal Intestine Small	intestine
11	chr4:124670000-124672600	Enhancers	Fetal Intestine Large	intestine
12	chr4:124670400-124671600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr4:124670400-124671800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:124670600-124671600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:124670600-124671600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:124670600-124671600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:124670600-124671600	Enhancers	Pancreas	Pancrea
18	chr4:124670600-124671600	Enhancers	HSMM	muscle
19	chr4:124670600-124671800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr4:124670600-124671800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:124670600-124671800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:124670600-124671800	Enhancers	Duodenum Mucosa	Duodenum
23	chr4:124670600-124672000	Enhancers	Hela-S3	cervix
24	chr4:124670600-124672000	Enhancers	HepG2	liver
25	chr4:124670800-124671800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:124670800-124671800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr4:124670800-124671800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:124671000-124671600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:124671000-124671800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:124671000-124671800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr4:124671000-124671800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr4:124671000-124671800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:124671000-124671800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr4:124671200-124671600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:124671200-124671600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:124671200-124671600	Enhancers	Placenta	Placenta
37	chr4:124671200-124671600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr4:124671200-124671600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr4:124671200-124671800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr4:124671200-124671800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:124671200-124671800	Enhancers	Fetal Kidney	kidney
42	chr4:124671200-124671800	Enhancers	Stomach Mucosa	stomach
43	chr4:124671200-124672000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:124671400-124671800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:124671400-124671800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:124671400-124673600	Weak transcription	Lung	lung

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