Variant report

Variant	rs2639712
Chromosome Location	chr1:225842940-225842941
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	CEBPB	chr1:225842894-225844100	IMR90	lung:	n/a	n/a
2	NFIC	chr1:225842634-225844138	ECC-1	luminal epithelium:	n/a	n/a
3	CEBPB	chr1:225842810-225844104	A549	lung:	n/a	n/a
4	STAT3	chr1:225842660-225843952	MCF10A-Er-Src	breast:	n/a	chr1:225843253-225843264 chr1:225843764-225843771 chr1:225843255-225843278
5	GATA3	chr1:225842875-225844244	A549	lung:	n/a	n/a
6	STAT3	chr1:225842805-225843631	MCF10A-Er-Src	breast:	n/a	chr1:225843253-225843264 chr1:225843255-225843278
7	NFIC	chr1:225842652-225844209	ECC-1	luminal epithelium:	n/a	n/a
8	FOXM1	chr1:225842620-225844083	ECC-1	luminal epithelium:	n/a	n/a
9	FOS	chr1:225842721-225843968	MCF10A-Er-Src	breast:	n/a	chr1:225843306-225843317 chr1:225843305-225843312 chr1:225843305-225843313
10	ESR1	chr1:225842641-225843038	ECC-1	luminal epithelium:	n/a	n/a
11	FOSL1	chr1:225842917-225844088	HCT-116	colon:	n/a	chr1:225843306-225843317 chr1:225843305-225843312 chr1:225843305-225843313
12	MAX	chr1:225842801-225844105	A549	lung:	n/a	n/a
13	ZKSCAN1	chr1:225842885-225843838	Hela-S3	cervix:	n/a	n/a
14	ESR1	chr1:225842645-225843035	ECC-1	luminal epithelium:	n/a	n/a
15	CEBPB	chr1:225842872-225844107	Hela-S3	cervix:	n/a	n/a
16	ATF3	chr1:225842910-225843885	A549	lung:	n/a	n/a
17	MYC	chr1:225842669-225843836	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr1:225842902-225843735	MCF10A-Er-Src	breast:	n/a	chr1:225843306-225843317 chr1:225843305-225843312 chr1:225843305-225843313
19	FOSL2	chr1:225842769-225844054	A549	lung:	n/a	chr1:225843306-225843317 chr1:225843305-225843312 chr1:225843305-225843313
20	NR3C1	chr1:225842660-225842945	ECC-1	luminal epithelium:	n/a	n/a
21	TBP	chr1:225842924-225843875	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:225838660-225844042	MCF10A-Er-Src	breast:	n/a	n/a
23	TEAD4	chr1:225842639-225844170	ECC-1	luminal epithelium:	n/a	chr1:225843803-225843812
24	POLR2A	chr1:225840071-225843898	PANC-1	pancreas:	n/a	n/a
25	REST	chr1:225842877-225843912	A549	lung:	n/a	n/a
26	CEBPB	chr1:225842862-225843976	HCT-116	colon:	n/a	n/a
27	SIX5	chr1:225842904-225844028	A549	lung:	n/a	n/a
28	FOS	chr1:225842799-225844029	MCF10A-Er-Src	breast:	n/a	chr1:225843306-225843317 chr1:225843305-225843312 chr1:225843305-225843313
29	KAP1	chr1:225842922-225843893	HEK293	kidney:	n/a	chr1:225843303-225843312
30	TEAD4	chr1:225842936-225843960	SK-N-SH	brain:	n/a	chr1:225843803-225843812
31	ZNF274	chr1:225842737-225843305	K562	blood:	n/a	n/a
32	CEBPB	chr1:225842861-225844052	A549	lung:	n/a	n/a
33	TCF12	chr1:225842825-225844152	SK-N-SH	brain:	n/a	n/a
34	PBX3	chr1:225842919-225844061	SK-N-SH	brain:	n/a	n/a
35	MYC	chr1:225842791-225843880	MCF10A-Er-Src	breast:	n/a	n/a
36	BCL3	chr1:225842650-225844106	A549	lung:	n/a	n/a
37	SMARCC1	chr1:225842855-225843951	Hela-S3	cervix:	n/a	n/a
38	KAP1	chr1:225842828-225843839	U2OS	brain:	n/a	chr1:225843303-225843312
39	E2F4	chr1:225842765-225843681	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr1:225842555-225843665	U87	brain:	n/a	n/a
41	TCF12	chr1:225842828-225844196	A549	lung:	n/a	n/a
42	MAX	chr1:225842642-225843923	ECC-1	luminal epithelium:	n/a	n/a
43	STAT3	chr1:225842766-225844029	MCF10A-Er-Src	breast:	n/a	chr1:225843253-225843264 chr1:225843764-225843771 chr1:225843255-225843278
44	SP1	chr1:225842893-225843982	HCT-116	colon:	n/a	n/a
45	POLR2A	chr1:225842673-225843590	IMR90	lung:	n/a	n/a
46	JUN	chr1:225842929-225843916	Hela-S3	cervix:	n/a	chr1:225843306-225843317 chr1:225843305-225843312 chr1:225843305-225843313
47	RAD21	chr1:225842842-225843908	Hela-S3	cervix:	n/a	n/a
48	EP300	chr1:225842669-225844283	ECC-1	luminal epithelium:	n/a	n/a
49	NFIC	chr1:225842834-225844132	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr1:225842685-225843574	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:225841590..225843627-chr1:225887293..225890031,4	MCF-7	breast:
2	chr1:225842059..225843604-chr1:225963580..225966384,2	K562	blood:
3	chr1:225841158..225843185-chr1:226308432..226310542,2	MCF-7	breast:
4	chr1:225840996..225843850-chr1:225947438..225950251,2	MCF-7	breast:
5	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:

Variant related genes	Relation type
ENAH	TF binding region
ENSG00000227496	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10799319	0.84[LWK][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs10915847	0.86[MEX][hapmap];0.81[TSI][hapmap]
rs1854286	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2639703	0.89[TSI][hapmap]
rs2639716	0.82[EUR][1000 genomes]
rs2657569	0.82[EUR][1000 genomes]
rs2769690	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2840967	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2840968	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3820226	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs4653643	0.82[MEX][hapmap]
rs487591	0.82[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs576861	0.82[LWK][hapmap];0.81[TSI][hapmap]
rs6751	0.82[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs712062	0.82[LWK][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]

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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2639712	PYCR2	cis	cerebellum	SCAN
rs2639712	ENAH	cis	normal skin	skin_eQTL
rs2639712	C1orf95	cis	cerebellum	SCAN
rs2639712	RP11-496N12.9	cis	Thyroid	GTEx
rs2639712	LBR	cis	Artery Tibial	GTEx
rs2639712	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225841400-225843000	Active TSS	Fetal Brain Male	brain
2	chr1:225841800-225843000	Enhancers	Hela-S3	cervix
3	chr1:225841800-225843200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr1:225841800-225843200	Flanking Active TSS	NHEK	skin
5	chr1:225841800-225844000	Enhancers	Fetal Heart	heart
6	chr1:225841800-225845000	Weak transcription	Lung	lung
7	chr1:225842000-225843600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:225842000-225843600	Enhancers	Brain Substantia Nigra	brain
9	chr1:225842000-225843800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:225842000-225844000	Enhancers	HepG2	liver
11	chr1:225842000-225844400	Enhancers	Rectal Smooth Muscle	rectum
12	chr1:225842000-225845000	Weak transcription	Left Ventricle	heart
13	chr1:225842000-225845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:225842000-225845200	Weak transcription	Placenta	Placenta
15	chr1:225842000-225845200	Weak transcription	Ovary	ovary
16	chr1:225842000-225846000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:225842000-225865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:225842200-225843000	Enhancers	Fetal Lung	lung
19	chr1:225842200-225843000	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:225842200-225843200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:225842200-225843200	Enhancers	Brain Hippocampus Middle	brain
22	chr1:225842200-225843200	Weak transcription	Fetal Brain Female	brain
23	chr1:225842200-225843400	Enhancers	HUVEC	blood vessel
24	chr1:225842200-225844000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:225842200-225844000	Enhancers	Fetal Stomach	stomach
26	chr1:225842200-225844200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:225842200-225844200	Enhancers	Adipose Nuclei	Adipose
28	chr1:225842200-225844200	Enhancers	HSMMtube	muscle
29	chr1:225842200-225845200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:225842200-225845200	Enhancers	Colon Smooth Muscle	Colon
31	chr1:225842200-225845200	Weak transcription	Right Ventricle	heart
32	chr1:225842200-225845400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:225842200-225845400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:225842200-225845800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:225842200-225846000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:225842200-225846000	Enhancers	HMEC	breast
37	chr1:225842200-225846600	Enhancers	Fetal Muscle Leg	muscle
38	chr1:225842200-225847200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:225842400-225843200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:225842400-225843200	Weak transcription	Brain Angular Gyrus	brain
41	chr1:225842400-225843600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:225842400-225843800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:225842400-225845600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:225842600-225843000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr1:225842600-225843000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:225842600-225843200	Flanking Active TSS	Osteobl	bone
47	chr1:225842600-225843400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:225842600-225843600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr1:225842600-225844000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:225842600-225845200	Weak transcription	Right Atrium	heart

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