Variant report

Variant	rs739249
Chromosome Location	chr1:172419960-172419961
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	GATA3	chr1:172419512-172420777	MCF-7	breast:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
2	HEY1	chr1:172418150-172420083	HepG2	liver:	n/a	n/a
3	HNF4G	chr1:172419670-172420003	HepG2	liver:	n/a	chr1:172419813-172419827 chr1:172419814-172419826 chr1:172419811-172419826 chr1:172419813-172419827 chr1:172419814-172419827 chr1:172419814-172419826 chr1:172419813-172419826 chr1:172419811-172419829 chr1:172419814-172419826 chr1:172419813-172419828
4	EP300	chr1:172419603-172420044	HepG2	liver:	n/a	n/a
5	MAZ	chr1:172419919-172420582	K562	blood:	n/a	chr1:172420446-172420455
6	KAP1	chr1:172418771-172420713	HEK293	kidney:	n/a	chr1:172420445-172420454
7	CREB1	chr1:172418049-172420111	HepG2	liver:	n/a	n/a
8	NR2F2	chr1:172418858-172420695	K562	blood:	n/a	n/a
9	NR2F2	chr1:172419016-172419992	K562	blood:	n/a	n/a
10	POLR2A	chr1:172418279-172420393	HepG2	liver:	n/a	n/a
11	ZEB1	chr1:172417854-172420270	HepG2	liver:	n/a	chr1:172418210-172418221 chr1:172418038-172418049 chr1:172418471-172418479 chr1:172419031-172419038
12	RAD21	chr1:172419716-172419976	HepG2	liver:	n/a	chr1:172419781-172419791
13	POLR2A	chr1:172419955-172419973	HepG2	liver:	n/a	n/a
14	MXI1	chr1:172418847-172420065	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:172418315-172420143	HL-60	blood:	n/a	n/a
16	GATA3	chr1:172419643-172420603	MCF-7	breast:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
17	MAX	chr1:172418247-172420387	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:172418157-172420104	HepG2	liver:	n/a	n/a
19	MAZ	chr1:172418831-172420595	HepG2	liver:	n/a	chr1:172420446-172420455
20	TEAD4	chr1:172419182-172420120	HepG2	liver:	n/a	n/a
21	NR2F2	chr1:172419483-172420685	MCF-7	breast:	n/a	n/a
22	MYC	chr1:172419758-172420006	HepG2	liver:	n/a	n/a
23	CTCF	chr1:172417456-172420817	A549	lung:	n/a	chr1:172419229-172419247 chr1:172420251-172420259 chr1:172419777-172419790 chr1:172419234-172419242 chr1:172419231-172419252
24	ZNF217	chr1:172419800-172420593	MCF-7	breast:	n/a	n/a
25	RCOR1	chr1:172419030-172420642	K562	blood:	n/a	n/a
26	MAX	chr1:172418995-172420243	A549	lung:	n/a	n/a
27	MAX	chr1:172418918-172420046	HepG2	liver:	n/a	n/a
28	HEY1	chr1:172419558-172420001	HepG2	liver:	n/a	n/a
29	MYBL2	chr1:172418107-172419993	HepG2	liver:	n/a	n/a
30	MAX	chr1:172418976-172420383	MCF-7	breast:	n/a	n/a
31	ZNF143	chr1:172419919-172420349	K562	blood:	n/a	n/a
32	CHD2	chr1:172419807-172420027	HepG2	liver:	n/a	n/a
33	TCF7L2	chr1:172419268-172421000	HEK293	kidney:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
34	TCF7L2	chr1:172419951-172420846	HepG2	liver:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
35	GATA3	chr1:172417920-172420674	MCF-7	breast:	n/a	chr1:172418403-172418412 chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172418190-172418211 chr1:172420461-172420471 chr1:172420223-172420232
36	RAD21	chr1:172418861-172420176	MCF-7	breast:	n/a	chr1:172419230-172419249 chr1:172419232-172419239 chr1:172419781-172419791
37	GATA1	chr1:172419113-172420914	PBDE	blood:	n/a	chr1:172420461-172420468 chr1:172420893-172420904 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
38	MYC	chr1:172419939-172420302	K562	blood:	n/a	n/a
39	POLR2A	chr1:172419540-172420000	HepG2	liver:	n/a	n/a
40	TCF7L2	chr1:172417976-172420696	Hela-S3	cervix:	n/a	chr1:172418405-172418414 chr1:172418727-172418736 chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172418724-172418740 chr1:172418725-172418739 chr1:172420413-172420429
41	MAX	chr1:172418231-172420178	HepG2	liver:	n/a	n/a
42	FOSL2	chr1:172419794-172420698	A549	lung:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172419909-172419921 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
43	BHLHE40	chr1:172419727-172419998	HepG2	liver:	n/a	n/a
44	TCF12	chr1:172417909-172420747	A549	lung:	n/a	chr1:172419611-172419618 chr1:172419480-172419490
45	POLR2A	chr1:172418384-172420817	PBDE	blood:	n/a	n/a
46	POLR2A	chr1:172418071-172420575	HepG2	liver:	n/a	n/a
47	MAFF	chr1:172419868-172420094	HepG2	liver:	n/a	n/a
48	MAX	chr1:172419059-172420078	K562	blood:	n/a	n/a
49	RCOR1	chr1:172418259-172420675	IMR90	lung:	n/a	n/a
50	BHLHE40	chr1:172418211-172420075	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172419256..172421468-chr1:172500783..172504604,4	K562	blood:
2	chr1:172418197..172419975-chr1:172480214..172481768,2	MCF-7	breast:
3	chr1:172416845..172420491-chr1:172421660..172424212,3	MCF-7	breast:
4	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
5	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:

Variant related genes	Relation type
C1orf105	TF binding region
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1009802	1.00[CHD][hapmap]
rs1129942	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16844417	1.00[CHD][hapmap]
rs17278379	1.00[CHD][hapmap]
rs17369123	0.84[CEU][hapmap]
rs2001130	0.89[EUR][1000 genomes]
rs2001132	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2213738	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs2901655	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3948765	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4244193	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4244194	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4916187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4916260	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4916261	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6660798	0.83[EUR][1000 genomes]
rs6689291	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7515895	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518300	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7522692	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7538417	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7544376	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551242	1.00[CHD][hapmap]
rs9425328	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425330	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs9425620	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947449	chr1:172419586-172424910	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs739249	GPA33	cis	parietal	SCAN
rs739249	RAGE	trans	lymphoblastoid	seeQTL
rs739249	VAMP4	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:172415400-172420000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:172415400-172420400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:172416400-172420000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:172416400-172420600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:172416400-172420600	Enhancers	HMEC	breast
8	chr1:172417200-172420600	Enhancers	NHEK	skin
9	chr1:172417200-172421800	Weak transcription	Psoas Muscle	Psoas
10	chr1:172417200-172423200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr1:172417600-172420800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:172417800-172420600	Enhancers	Placenta	Placenta
13	chr1:172417800-172420600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:172417800-172420800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:172417800-172420800	Enhancers	Fetal Kidney	kidney
16	chr1:172418000-172420200	Flanking Active TSS	A549	lung
17	chr1:172418000-172420400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:172418000-172420400	Enhancers	Stomach Mucosa	stomach
19	chr1:172418000-172420800	Enhancers	HUVEC	blood vessel
20	chr1:172418000-172422200	Enhancers	NH-A	brain
21	chr1:172418400-172420400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:172418400-172420600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:172418600-172420200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:172418600-172420400	Enhancers	Esophagus	oesophagus
25	chr1:172418800-172420000	Enhancers	Fetal Muscle Trunk	muscle
26	chr1:172418800-172420000	Enhancers	Lung	lung
27	chr1:172418800-172420200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:172418800-172420400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:172418800-172420400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:172418800-172420400	Enhancers	Left Ventricle	heart
31	chr1:172418800-172420600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:172419000-172420000	Enhancers	Brain Anterior Caudate	brain
33	chr1:172419000-172420000	Enhancers	Ovary	ovary
34	chr1:172419000-172420000	Enhancers	Hela-S3	cervix
35	chr1:172419000-172420400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr1:172419000-172420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:172419000-172420400	Enhancers	Pancreas	Pancrea
38	chr1:172419000-172420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:172419000-172420600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:172419000-172420600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:172419000-172420600	Enhancers	Liver	Liver
42	chr1:172419000-172420600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:172419000-172420600	Enhancers	NHLF	lung
44	chr1:172419200-172420000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:172419200-172420000	Active TSS	HepG2	liver
46	chr1:172419200-172420200	Active TSS	Rectal Smooth Muscle	rectum
47	chr1:172419200-172420400	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr1:172419200-172420400	Enhancers	Dnd41	blood
49	chr1:172419200-172420600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:172419200-172420800	Enhancers	Fetal Heart	heart

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