Variant report

Variant	rs4916187
Chromosome Location	chr1:172419615-172419616
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	ARID3A	chr1:172418036-172419866	HepG2	liver:	n/a	n/a
2	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
3	MBD4	chr1:172418944-172419693	HepG2	liver:	n/a	n/a
4	CTCF	chr1:172419540-172419690	GM12872	blood:	n/a	n/a
5	HEY1	chr1:172418150-172420083	HepG2	liver:	n/a	n/a
6	EP300	chr1:172419603-172420044	HepG2	liver:	n/a	n/a
7	KAP1	chr1:172418771-172420713	HEK293	kidney:	n/a	chr1:172420445-172420454
8	CREB1	chr1:172418049-172420111	HepG2	liver:	n/a	n/a
9	NR2F2	chr1:172418858-172420695	K562	blood:	n/a	n/a
10	POLR2A	chr1:172418326-172419862	HepG2	liver:	n/a	n/a
11	NR2F2	chr1:172419016-172419992	K562	blood:	n/a	n/a
12	CTCF	chr1:172419560-172419710	HCPEpiC	choroid plexus:	n/a	n/a
13	POLR2A	chr1:172418279-172420393	HepG2	liver:	n/a	n/a
14	ZEB1	chr1:172417854-172420270	HepG2	liver:	n/a	chr1:172418210-172418221 chr1:172418038-172418049 chr1:172418471-172418479 chr1:172419031-172419038
15	RAD21	chr1:172418690-172419675	A549	lung:	n/a	chr1:172419230-172419249 chr1:172419232-172419239
16	RAD21	chr1:172418928-172419616	ECC-1	luminal epithelium:	n/a	chr1:172419230-172419249 chr1:172419232-172419239
17	CTCF	chr1:172419600-172419750	SK-N-SH_RA	brain:	n/a	n/a
18	MXI1	chr1:172418847-172420065	HepG2	liver:	n/a	n/a
19	SMC3	chr1:172418328-172419761	SK-N-SH	brain:	n/a	chr1:172419231-172419245
20	POLR2A	chr1:172418315-172420143	HL-60	blood:	n/a	n/a
21	CHD2	chr1:172418807-172419616	K562	blood:	n/a	n/a
22	MAX	chr1:172418247-172420387	HepG2	liver:	n/a	n/a
23	CTCF	chr1:172418684-172419707	SK-N-SH	brain:	n/a	chr1:172419229-172419247 chr1:172419234-172419242 chr1:172419231-172419252
24	POLR2A	chr1:172418157-172420104	HepG2	liver:	n/a	n/a
25	MAZ	chr1:172418831-172420595	HepG2	liver:	n/a	chr1:172420446-172420455
26	TEAD4	chr1:172419182-172420120	HepG2	liver:	n/a	n/a
27	NR2F2	chr1:172419483-172420685	MCF-7	breast:	n/a	n/a
28	CBX3	chr1:172418843-172419702	K562	blood:	n/a	n/a
29	CTCF	chr1:172417456-172420817	A549	lung:	n/a	chr1:172419229-172419247 chr1:172420251-172420259 chr1:172419777-172419790 chr1:172419234-172419242 chr1:172419231-172419252
30	RCOR1	chr1:172419030-172420642	K562	blood:	n/a	n/a
31	MAX	chr1:172418995-172420243	A549	lung:	n/a	n/a
32	MAX	chr1:172418918-172420046	HepG2	liver:	n/a	n/a
33	HEY1	chr1:172419558-172420001	HepG2	liver:	n/a	n/a
34	CTCF	chr1:172418755-172419684	HCT-116	colon:	n/a	chr1:172419229-172419247 chr1:172419234-172419242 chr1:172419231-172419252
35	CTCF	chr1:172419560-172419710	HBMEC	blood vessel:	n/a	n/a
36	MYBL2	chr1:172418107-172419993	HepG2	liver:	n/a	n/a
37	MAX	chr1:172418976-172420383	MCF-7	breast:	n/a	n/a
38	NFIC	chr1:172419028-172419751	HepG2	liver:	n/a	n/a
39	MYBL2	chr1:172418172-172419894	HepG2	liver:	n/a	n/a
40	ZC3H11A	chr1:172419035-172419899	K562	blood:	n/a	n/a
41	ZNF143	chr1:172419013-172419628	K562	blood:	n/a	n/a
42	ELK1	chr1:172418966-172419631	K562	blood:	n/a	n/a
43	RAD21	chr1:172418821-172419685	SK-N-SH	brain:	n/a	chr1:172419230-172419249 chr1:172419232-172419239
44	JUND	chr1:172418245-172419711	K562	blood:	n/a	chr1:172418404-172418414 chr1:172418403-172418414 chr1:172418404-172418414 chr1:172418405-172418413 chr1:172418403-172418415
45	TBL1XR1	chr1:172418793-172419645	K562	blood:	n/a	n/a
46	TCF7L2	chr1:172419268-172421000	HEK293	kidney:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
47	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
48	RAD21	chr1:172418819-172419677	HCT-116	colon:	n/a	chr1:172419230-172419249 chr1:172419232-172419239
49	RAD21	chr1:172418861-172420176	MCF-7	breast:	n/a	chr1:172419230-172419249 chr1:172419232-172419239 chr1:172419781-172419791
50	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

No.	Distal block	Cell Line	Cell type
1	chr1:172418092..172419733-chr1:172445872..172448682,2	MCF-7	breast:
2	chr1:172419256..172421468-chr1:172500783..172504604,4	K562	blood:
3	chr1:172418197..172419975-chr1:172480214..172481768,2	MCF-7	breast:
4	chr1:172416845..172420491-chr1:172421660..172424212,3	MCF-7	breast:
5	chr1:172398325..172399061-chr1:172419028..172419711,2	MCF-7	breast:
6	chr1:172419133..172419664-chr1:172696878..172697829,2	K562	blood:
7	chr1:172418751..172419643-chr1:172696748..172697418,2	MCF-7	breast:
8	chr1:172418550..172419714-chr1:172502016..172503069,7	MCF-7	breast:
9	chr1:172419156..172419700-chr1:172503275..172503932,2	MCF-7	breast:
10	chr1:172418801..172419669-chr1:172502176..172502929,3	MCF-7	breast:
11	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
12	chr1:172418751..172419678-chr1:172500342..172501547,4	MCF-7	breast:
13	chr1:172418589..172419710-chr1:172688502..172689393,4	MCF-7	breast:
14	chr1:172327243..172328745-chr1:172418219..172419831,2	MCF-7	breast:
15	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:
16	chr1:172418803..172419732-chr1:172578542..172579221,4	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: 2 )

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]
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]
rs739249	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]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4916187	GPA33	cis	parietal	SCAN
rs4916187	VAMP4	cis	cerebellum	SCAN

Chromatin state (count:90 , 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	chr1:172416400-172419800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:172416400-172419800	Enhancers	Fetal Intestine Small	intestine
7	chr1:172416400-172420000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr1:172416400-172420600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:172416400-172420600	Enhancers	HMEC	breast
10	chr1:172417200-172420600	Enhancers	NHEK	skin
11	chr1:172417200-172421800	Weak transcription	Psoas Muscle	Psoas
12	chr1:172417200-172423200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr1:172417600-172420800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:172417800-172420600	Enhancers	Placenta	Placenta
15	chr1:172417800-172420600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:172417800-172420800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:172417800-172420800	Enhancers	Fetal Kidney	kidney
18	chr1:172418000-172420200	Flanking Active TSS	A549	lung
19	chr1:172418000-172420400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:172418000-172420400	Enhancers	Stomach Mucosa	stomach
21	chr1:172418000-172420800	Enhancers	HUVEC	blood vessel
22	chr1:172418000-172422200	Enhancers	NH-A	brain
23	chr1:172418400-172420400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:172418400-172420600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:172418600-172419800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:172418600-172420200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:172418600-172420400	Enhancers	Esophagus	oesophagus
28	chr1:172418800-172420000	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:172418800-172420000	Enhancers	Lung	lung
30	chr1:172418800-172420200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr1:172418800-172420400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:172418800-172420400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:172418800-172420400	Enhancers	Left Ventricle	heart
34	chr1:172418800-172420600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:172419000-172419800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:172419000-172419800	Enhancers	Fetal Thymus	thymus
37	chr1:172419000-172419800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:172419000-172420000	Enhancers	Brain Anterior Caudate	brain
39	chr1:172419000-172420000	Enhancers	Ovary	ovary
40	chr1:172419000-172420000	Enhancers	Hela-S3	cervix
41	chr1:172419000-172420400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr1:172419000-172420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr1:172419000-172420400	Enhancers	Pancreas	Pancrea
44	chr1:172419000-172420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:172419000-172420600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:172419000-172420600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:172419000-172420600	Enhancers	Liver	Liver
48	chr1:172419000-172420600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:172419000-172420600	Enhancers	NHLF	lung
50	chr1:172419200-172419800	Flanking Active TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links