Variant report

Variant	rs769235
Chromosome Location	chr4:122745193-122745194
allele	G/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	POLR2A	chr4:122743985-122745536	GM12878	blood:	n/a	n/a
2	MXI1	chr4:122743533-122745750	IMR90	lung:	n/a	n/a
3	SIN3AK20	chr4:122744574-122745550	HCT-116	colon:	n/a	n/a
4	POLR2A	chr4:122744778-122745442	PANC-1	pancreas:	n/a	n/a
5	CEBPB	chr4:122744512-122745336	ECC-1	luminal epithelium:	n/a	n/a
6	TAF1	chr4:122744528-122745449	H1-hESC	embryonic stem cell:	n/a	n/a
7	ETS1	chr4:122744542-122745282	K562	blood:	n/a	n/a
8	FOS	chr4:122745090-122745287	MCF10A-Er-Src	breast:	n/a	chr4:122745227-122745236
9	POLR2A	chr4:122745185-122745365	A549	lung:	n/a	n/a
10	MYC	chr4:122744888-122745304	K562	blood:	n/a	n/a
11	TAL1	chr4:122743798-122745738	K562	blood:	n/a	n/a
12	NR2F2	chr4:122744451-122745471	K562	blood:	n/a	n/a
13	HDAC2	chr4:122744845-122745232	HepG2	liver:	n/a	n/a
14	GTF2F1	chr4:122744814-122745502	K562	blood:	n/a	n/a
15	RFX5	chr4:122744881-122745518	Hela-S3	cervix:	n/a	n/a
16	SIN3AK20	chr4:122744649-122745276	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:122743956-122745788	PFSK-1	brain:	n/a	n/a
18	SIN3AK20	chr4:122743880-122745547	MCF-7	breast:	n/a	n/a
19	SRF	chr4:122744890-122745321	GM12878	blood:	n/a	n/a
20	BRCA1	chr4:122744956-122745262	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:122743960-122745630	GM18505	blood:	n/a	n/a
22	CEBPB	chr4:122744531-122745394	Hela-S3	cervix:	n/a	n/a
23	MAX	chr4:122744582-122745572	HCT-116	colon:	n/a	n/a
24	SIN3AK20	chr4:122743965-122745319	K562	blood:	n/a	n/a
25	CREB1	chr4:122743717-122745581	K562	blood:	n/a	n/a
26	POLR2A	chr4:122744690-122745362	H1-neurons	neurons:	n/a	n/a
27	ATF3	chr4:122744867-122745251	H1-hESC	embryonic stem cell:	n/a	chr4:122745109-122745120 chr4:122745111-122745122 chr4:122745109-122745119 chr4:122745112-122745120 chr4:122745109-122745122 chr4:122745112-122745119 chr4:122745228-122745237
28	POLR2A	chr4:122744278-122745670	HUVEC	blood vessel:	n/a	n/a
29	MYC	chr4:122743875-122745485	K562	blood:	n/a	n/a
30	MAX	chr4:122744411-122745389	MCF-7	breast:	n/a	n/a
31	NRF1	chr4:122744434-122745789	SK-N-SH	brain:	n/a	chr4:122745218-122745229 chr4:122745220-122745229
32	NFIC	chr4:122744919-122745254	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr4:122744458-122745378	MCF-7	breast:	n/a	n/a
34	CTCF	chr4:122745160-122745310	MCF-7	breast:	n/a	chr4:122745286-122745293
35	TAF1	chr4:122745172-122745385	GM12878	blood:	n/a	n/a
36	SRF	chr4:122744834-122745446	MCF-7	breast:	n/a	n/a
37	POLR2A	chr4:122743954-122745495	GM19193	blood:	n/a	n/a
38	RELA	chr4:122743973-122745482	GM15510	blood:	n/a	n/a
39	POU2F2	chr4:122744819-122745436	GM12891	blood:	n/a	chr4:122745171-122745183
40	POLR2A	chr4:122744727-122745565	HUVEC	blood vessel:	n/a	n/a
41	RELA	chr4:122744907-122745474	GM19099	blood:	n/a	n/a
42	ZNF143	chr4:122744869-122745485	GM12878	blood:	n/a	n/a
43	TAF1	chr4:122744970-122745387	SK-N-SH	brain:	n/a	n/a
44	ELF1	chr4:122744471-122745346	HepG2	liver:	n/a	chr4:122744672-122744685 chr4:122745171-122745183 chr4:122745203-122745215
45	MAX	chr4:122744796-122745212	A549	lung:	n/a	n/a
46	YY1	chr4:122744848-122745282	GM12878	blood:	n/a	n/a
47	ATF3	chr4:122744884-122745383	HepG2	liver:	n/a	chr4:122745109-122745120 chr4:122745111-122745122 chr4:122745109-122745119 chr4:122745112-122745120 chr4:122745109-122745122 chr4:122745112-122745119 chr4:122745228-122745237
48	NFYB	chr4:122744189-122745387	K562	blood:	n/a	chr4:122745082-122745097 chr4:122745085-122745099 chr4:122745084-122745096 chr4:122745085-122745100
49	TBL1XR1	chr4:122744962-122745569	GM12878	blood:	n/a	n/a
50	PAX5	chr4:122744888-122745304	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:122743728..122745720-chr4:123072564..123074276,2	MCF-7	breast:
2	chr4:122730694..122733208-chr4:122742795..122745639,3	MCF-7	breast:
3	chr4:122743665..122745647-chr4:122789959..122792844,2	K562	blood:
4	chr4:122745115..122747989-chr4:122763596..122768679,4	K562	blood:
5	chr4:122743937..122745709-chr4:122789073..122792833,3	MCF-7	breast:
6	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
7	chr4:122722789..122724421-chr4:122743647..122745561,2	MCF-7	breast:
8	chr14:34419446..34420192-chr4:122744900..122745700,2	Hela-S3	cervix:
9	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:

Variant related genes	Relation type
CCNA2	TF binding region
ENSG00000261501	Chromatin interaction
ENSG00000138688	Chromatin interaction
ENSG00000138686	Chromatin interaction
ENSG00000129521	Chromatin interaction
ENSG00000123737	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11930245	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11930756	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11933339	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11934168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11942369	1.00[EUR][1000 genomes]
rs1507987	1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs1507988	0.83[AMR][1000 genomes]
rs17005269	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005276	0.83[ASW][hapmap];0.85[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2661556	0.83[AMR][1000 genomes]
rs2706797	0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs3217770	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34669312	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3811743	0.83[AMR][1000 genomes]
rs4001033	0.83[AMR][1000 genomes]
rs4075713	0.91[GIH][hapmap]
rs4132552	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61639241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6845842	1.00[EUR][1000 genomes]
rs72915930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915943	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72917987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72917996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72918000	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs769240	0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr4:122742600-122745400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:122742600-122745600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:122742800-122745600	Active TSS	Thymus	Thymus
4	chr4:122742800-122745600	Active TSS	NHLF	lung
5	chr4:122743400-122745600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:122743400-122745600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:122743400-122745600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:122743400-122745600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:122743400-122745600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:122743400-122745800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr4:122743600-122745400	Active TSS	HSMM	muscle
12	chr4:122743600-122745600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:122743600-122745600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:122743600-122745600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:122743600-122745600	Active TSS	Fetal Intestine Small	intestine
16	chr4:122743600-122745600	Active TSS	Hela-S3	cervix
17	chr4:122743600-122745800	Active TSS	Fetal Intestine Large	intestine
18	chr4:122743600-122745800	Active TSS	NHDF-Ad	bronchial
19	chr4:122743800-122745400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:122743800-122745400	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr4:122743800-122745400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:122743800-122745400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:122743800-122745400	Active TSS	Osteobl	bone
24	chr4:122743800-122745600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr4:122743800-122745600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:122743800-122745600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:122743800-122745600	Active TSS	HSMMtube	muscle
28	chr4:122743800-122745800	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr4:122743800-122745800	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr4:122743800-122745800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:122743800-122745800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:122743800-122745800	Active TSS	GM12878-XiMat	blood
33	chr4:122744000-122745400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr4:122744000-122745400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:122744000-122745400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr4:122744000-122745400	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr4:122744000-122745400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr4:122744000-122745600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:122744000-122745600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr4:122744000-122745600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr4:122744000-122745600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:122744000-122745600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:122744000-122745600	Active TSS	Fetal Heart	heart
44	chr4:122744000-122745600	Active TSS	Fetal Kidney	kidney
45	chr4:122744000-122745600	Active TSS	Rectal Smooth Muscle	rectum
46	chr4:122744000-122745600	Active TSS	NH-A	brain
47	chr4:122744000-122745800	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr4:122744000-122745800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr4:122744000-122745800	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr4:122744000-122745800	Active TSS	Pancreatic Islets	Pancreatic Islet

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