Variant report

Variant	rs3806792
Chromosome Location	chr4:74965274-74965275
allele	C/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	MAZ	chr4:74963369-74965651	Hela-S3	cervix:	n/a	chr4:74965045-74965055
2	GATA3	chr4:74964982-74965334	T-47D	breast:	n/a	n/a
3	ATF3	chr4:74964820-74965387	A549	lung:	n/a	chr4:74965072-74965082 chr4:74965060-74965080
4	FOS	chr4:74964941-74965639	MCF10A-Er-Src	breast:	n/a	chr4:74964959-74964973
5	POLR2A	chr4:74961030-74966092	HUVEC	blood vessel:	n/a	n/a
6	NR3C1	chr4:74964879-74965855	A549	lung:	n/a	n/a
7	FOS	chr4:74964994-74965623	HUVEC	blood vessel:	n/a	n/a
8	SMARCB1	chr4:74963518-74965807	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr4:74964735-74965777	K562	blood:	n/a	chr4:74965090-74965103
10	YY1	chr4:74964890-74965343	A549	lung:	n/a	n/a
11	GATA3	chr4:74964807-74965705	A549	lung:	n/a	chr4:74965349-74965356 chr4:74965349-74965356 chr4:74965342-74965363 chr4:74965345-74965361 chr4:74965349-74965356 chr4:74965346-74965356
12	CREB1	chr4:74964867-74965760	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:74960198-74966096	MCF10A-Er-Src	breast:	n/a	n/a
14	MXI1	chr4:74964995-74965294	K562	blood:	n/a	n/a
15	POLR2A	chr4:74964761-74965363	HL-60	blood:	n/a	n/a
16	FOS	chr4:74964921-74965658	MCF10A-Er-Src	breast:	n/a	chr4:74964959-74964973
17	MAX	chr4:74962915-74965899	Hela-S3	cervix:	n/a	chr4:74965045-74965055
18	MAX	chr4:74964763-74965658	SK-N-SH	brain:	n/a	chr4:74965045-74965055
19	POLR2A	chr4:74964573-74965285	A549	lung:	n/a	n/a
20	HEY1	chr4:74964202-74965441	K562	blood:	n/a	n/a
21	MAX	chr4:74965123-74965437	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr4:74964791-74965563	HepG2	liver:	n/a	n/a
23	GATA3	chr4:74964889-74965519	SK-N-SH	brain:	n/a	chr4:74965349-74965356 chr4:74965349-74965356 chr4:74965342-74965363 chr4:74965345-74965361 chr4:74965349-74965356 chr4:74965346-74965356
24	TAF1	chr4:74964447-74965325	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPB	chr4:74964740-74965316	H1-hESC	embryonic stem cell:	n/a	chr4:74965090-74965103
26	GTF2F1	chr4:74964771-74965827	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr4:74964478-74965341	H1-hESC	embryonic stem cell:	n/a	n/a
28	YY1	chr4:74964377-74965330	K562	blood:	n/a	n/a
29	MAX	chr4:74964172-74965565	K562	blood:	n/a	chr4:74965045-74965055
30	CEBPB	chr4:74964687-74965783	K562	blood:	n/a	chr4:74965090-74965103
31	CHD2	chr4:74961899-74965770	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr4:74964279-74965537	H1-hESC	embryonic stem cell:	n/a	n/a
33	FOXA2	chr4:74964911-74965351	A549	lung:	n/a	n/a
34	UBTF	chr4:74964259-74965351	K562	blood:	n/a	n/a
35	HA-E2F1	chr4:74964962-74965902	MCF-7	breast:	n/a	n/a
36	TAF1	chr4:74964741-74965366	K562	blood:	n/a	n/a
37	POLR2A	chr4:74962724-74965809	U87	brain:	n/a	n/a
38	SP1	chr4:74964636-74965890	A549	lung:	n/a	chr4:74965031-74965040 chr4:74965030-74965042 chr4:74965030-74965042
39	JUND	chr4:74964825-74965301	H1-hESC	embryonic stem cell:	n/a	chr4:74964959-74964973
40	JUN	chr4:74964823-74965600	K562	blood:	n/a	chr4:74964959-74964973
41	POLR2A	chr4:74963429-74965586	PBDE	blood:	n/a	n/a
42	POLR2A	chr4:74964622-74965390	K562	blood:	n/a	n/a
43	USF1	chr4:74965127-74965678	A549	lung:	n/a	chr4:74965495-74965506
44	GTF2B	chr4:74964915-74965330	K562	blood:	n/a	n/a
45	POLR2A	chr4:74965062-74965326	H1-hESC	embryonic stem cell:	n/a	n/a
46	GABPA	chr4:74965207-74965691	A549	lung:	n/a	n/a
47	CEBPB	chr4:74964943-74965309	MCF-7	breast:	n/a	chr4:74965090-74965103
48	BCL3	chr4:74964782-74965778	A549	lung:	n/a	chr4:74964980-74964989
49	NR3C1	chr4:74964936-74965603	A549	lung:	n/a	n/a
50	POLR2A	chr4:74964778-74965389	Gliobla	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:74965226-74965276	HEK293	kidney:	embryo
2	chr4:74965226-74965276	AoSMC	blood vessel:	n/a
3	chr4:74965226-74965276	PFSK-1	brain:	n/a
4	chr4:74965262-74965312	AG09319	gingival:	n/a
5	chr4:74965226-74965276	HCF	heart:	n/a
6	chr4:74965226-74965276	AG10803	skin:	n/a
7	chr4:74965262-74965312	GM12891	blood:	n/a
8	chr4:74965262-74965312	IMR90	lung:	fetal
9	chr4:74965262-74965312	BJ	skin:	n/a
10	chr4:74965262-74965312	Hela-S3	cervix:	n/a
11	chr4:74965262-74965312	HUVEC	blood vessel:	n/a
12	chr4:74965262-74965312	A549	lung:	n/a
13	chr4:74965262-74965312	HPAEpiC	pulmonary alveolar:	n/a
14	chr4:74965262-74965312	HCF	heart:	n/a
15	chr4:74965262-74965312	NHDF-neo	bronchial:	n/a
16	chr4:74965226-74965276	MCF10A-Er-Src	breast:	n/a
17	chr4:74965226-74965276	HCT-116	colon:	n/a
18	chr4:74965262-74965312	K562	blood:	n/a
19	chr4:74965262-74965312	AoSMC	blood vessel:	n/a
20	chr4:74965262-74965312	HIPEpiC	eye:	n/a
21	chr4:74965262-74965312	GM19239	blood:	n/a
22	chr4:74965262-74965312	GM12878	blood:	n/a
23	chr4:74965262-74965312	NB4	blood:	n/a
24	chr4:74965226-74965276	HL-60	blood:	n/a
25	chr4:74965262-74965312	ProgFib	skin:	n/a
26	chr4:74965226-74965276	HepG2	liver:	n/a
27	chr4:74965226-74965276	AG09309	skin:	n/a
28	chr4:74965226-74965276	Jurkat	blood:	n/a
29	chr4:74965226-74965276	NT2-D1	testis:	n/a
30	chr4:74965226-74965276	GM12891	blood:	n/a
31	chr4:74965226-74965276	GM19239	blood:	n/a
32	chr4:74965226-74965276	Hepatocyte	liver:	n/a
33	chr4:74965226-74965276	RPTEC	kidney:	n/a
34	chr4:74965226-74965276	HRE	kidney:	n/a
35	chr4:74965226-74965276	HCM	heart:	n/a
36	chr4:74965262-74965312	SK-N-SH_RA	brain:	n/a
37	chr4:74965262-74965312	Jurkat	blood:	n/a
38	chr4:74965262-74965312	HEK293	kidney:	embryo
39	chr4:74965226-74965276	GM06990	blood:	n/a
40	chr4:74965226-74965276	ProgFib	skin:	n/a
41	chr4:74965262-74965312	GM12892	blood:	n/a
42	chr4:74965262-74965312	HL-60	blood:	n/a
43	chr4:74965226-74965276	SK-N-SH_RA	brain:	n/a
44	chr4:74965226-74965276	HRCEpiC	kidney:	n/a
45	chr4:74965262-74965312	AG09309	skin:	n/a
46	chr4:74965226-74965276	AG09319	gingival:	n/a
47	chr4:74965226-74965276	K562	blood:	n/a
48	chr4:74965226-74965276	NHDF-neo	bronchial:	n/a
49	chr4:74965226-74965276	BE2_C	brain:	n/a
50	chr4:74965262-74965312	SK-N-MC	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:74962349..74965298-chr4:74989325..74991389,2	K562	blood:
2	chr4:74917692..74925936-chr4:74958187..74967502,26	K562	blood:
3	chr4:74918446..74926481-chr4:74958079..74968779,32	K562	blood:
4	chr4:74851739..74854403-chr4:74963731..74965343,2	K562	blood:
5	chr4:74964506..74967065-chr4:75022087..75025561,3	K562	blood:
6	chr4:74964506..74968474-chr4:75022087..75025768,6	K562	blood:
7	chr4:74902918..74906977-chr4:74963214..74968788,8	K562	blood:
8	chr4:74903038..74905484-chr4:74963526..74965321,3	K562	blood:

Variant related genes	Relation type
CXCL2	TF binding region
CXCL2	CpG island
ENSG00000248848	Chromatin interaction
ENSG00000163734	Chromatin interaction
ENSG00000269559	Chromatin interaction
ENSG00000163738	Chromatin interaction
ENSG00000163736	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10938107	0.87[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs11725704	0.81[EUR][1000 genomes]
rs11733208	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12642974	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs13124617	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128896	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1371794	0.81[EUR][1000 genomes]
rs1371798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1837559	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs1866755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4121652	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491641	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs518867	0.81[EUR][1000 genomes]
rs546829	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs549280	0.94[EUR][1000 genomes]
rs72652928	0.80[EUR][1000 genomes]
rs72652934	0.93[EUR][1000 genomes]
rs7667376	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7684973	0.91[JPT][hapmap]
rs7686861	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs882638	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9131	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981458	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3806792	CCNG2	cis	parietal	SCAN
rs3806792	CXCL6	cis	parietal	SCAN
rs3806792	UTP3	cis	parietal	SCAN
rs3806792	G3BP2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74962800-74965400	Active TSS	A549	lung
2	chr4:74962800-74965600	Active TSS	Right Atrium	heart
3	chr4:74963000-74965400	Active TSS	Left Ventricle	heart
4	chr4:74963000-74965600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:74963000-74965600	Active TSS	Psoas Muscle	Psoas
6	chr4:74963400-74965400	Active TSS	Rectal Smooth Muscle	rectum
7	chr4:74963400-74965600	Active TSS	Brain Hippocampus Middle	brain
8	chr4:74963400-74965600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr4:74963400-74965600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr4:74963600-74965400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:74963600-74965400	Active TSS	Colonic Mucosa	Colon
12	chr4:74963600-74965800	Active TSS	Brain Substantia Nigra	brain
13	chr4:74963800-74965400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:74963800-74965400	Active TSS	Gastric	stomach
15	chr4:74963800-74965400	Active TSS	Lung	lung
16	chr4:74963800-74965400	Active TSS	Placenta Amnion	Placenta Amnion
17	chr4:74963800-74965400	Active TSS	Thymus	Thymus
18	chr4:74963800-74965400	Active TSS	NHDF-Ad	bronchial
19	chr4:74963800-74965600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr4:74963800-74965600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:74963800-74965600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:74963800-74965600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:74963800-74965600	Active TSS	Right Ventricle	heart
24	chr4:74963800-74965600	Active TSS	HSMMtube	muscle
25	chr4:74964000-74965400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:74964000-74965400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:74964000-74965400	Active TSS	Esophagus	oesophagus
28	chr4:74964000-74965400	Active TSS	Small Intestine	intestine
29	chr4:74964000-74965600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:74964200-74965400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr4:74964200-74965400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:74964200-74965400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:74964200-74965400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:74964200-74965400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:74964200-74965600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:74964200-74965600	Active TSS	Liver	Liver
37	chr4:74964200-74965600	Active TSS	Brain Angular Gyrus	brain
38	chr4:74964200-74965600	Active TSS	Brain Germinal Matrix	brain
39	chr4:74964200-74965600	Active TSS	NHLF	lung
40	chr4:74964200-74965800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr4:74964400-74965400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:74964400-74965400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:74964400-74965400	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
44	chr4:74964400-74965400	Active TSS	Aorta	Aorta
45	chr4:74964400-74965400	Active TSS	Colon Smooth Muscle	Colon
46	chr4:74964400-74965400	Active TSS	Duodenum Mucosa	Duodenum
47	chr4:74964400-74965400	Active TSS	Stomach Mucosa	stomach
48	chr4:74964400-74965600	Active TSS	Primary T cells from cord blood	blood
49	chr4:74964400-74965600	Active TSS	Fetal Kidney	kidney
50	chr4:74964600-74965400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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