Variant report

Variant	rs6673869
Chromosome Location	chr1:172420472-172420473
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	EP300	chr1:172420164-172420607	HepG2	liver:	n/a	chr1:172420565-172420575
2	JUND	chr1:172420340-172420501	HepG2	liver:	n/a	chr1:172420447-172420455 chr1:172420445-172420456 chr1:172420445-172420457
3	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
4	FOXA2	chr1:172420234-172420685	HepG2	liver:	n/a	chr1:172420470-172420482
5	FOSL2	chr1:172420199-172420571	HepG2	liver:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
6	SMC3	chr1:172419983-172420501	HepG2	liver:	n/a	n/a
7	MAZ	chr1:172419919-172420582	K562	blood:	n/a	chr1:172420446-172420455
8	MAZ	chr1:172419983-172420712	IMR90	lung:	n/a	chr1:172420446-172420455 chr1:172420649-172420658
9	KAP1	chr1:172418771-172420713	HEK293	kidney:	n/a	chr1:172420445-172420454
10	NR2F2	chr1:172418858-172420695	K562	blood:	n/a	n/a
11	GATA3	chr1:172420133-172420771	SK-N-SH	brain:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
12	SP1	chr1:172420134-172420664	A549	lung:	n/a	n/a
13	NR2F2	chr1:172420123-172420619	MCF-7	breast:	n/a	n/a
14	JUND	chr1:172420266-172420662	Hela-S3	cervix:	n/a	chr1:172420447-172420455 chr1:172420614-172420626 chr1:172420445-172420456 chr1:172420445-172420457
15	CTCF	chr1:172420420-172420570	HBMEC	blood vessel:	n/a	n/a
16	ARID3A	chr1:172420022-172420602	K562	blood:	n/a	n/a
17	TEAD4	chr1:172420194-172420709	HepG2	liver:	n/a	n/a
18	TCF7L2	chr1:172420165-172420608	PANC-1	pancreas:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
19	EP300	chr1:172420271-172420653	Hela-S3	cervix:	n/a	chr1:172420565-172420575
20	FOS	chr1:172420227-172420620	HUVEC	blood vessel:	n/a	chr1:172420447-172420455 chr1:172420445-172420456 chr1:172420445-172420457
21	HDAC2	chr1:172420246-172420558	HepG2	liver:	n/a	n/a
22	TBL1XR1	chr1:172420112-172420608	K562	blood:	n/a	n/a
23	RCOR1	chr1:172420269-172420529	Hela-S3	cervix:	n/a	n/a
24	FOXA1	chr1:172420162-172420768	HepG2	liver:	n/a	chr1:172420470-172420482 chr1:172420560-172420575
25	EP300	chr1:172420068-172420688	A549	lung:	n/a	chr1:172420565-172420575
26	RAD21	chr1:172420312-172420570	Hela-S3	cervix:	n/a	n/a
27	FOXA2	chr1:172420211-172420810	A549	lung:	n/a	chr1:172420470-172420482
28	IRF1	chr1:172420207-172420603	K562	blood:	n/a	chr1:172420567-172420581 chr1:172420446-172420455
29	MYBL2	chr1:172420232-172420651	HepG2	liver:	n/a	n/a
30	REST	chr1:172420182-172420680	A549	lung:	n/a	n/a
31	FOXA2	chr1:172420221-172420954	A549	lung:	n/a	chr1:172420470-172420482
32	SP1	chr1:172420024-172420693	A549	lung:	n/a	n/a
33	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
34	GATA3	chr1:172420002-172420856	A549	lung:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
35	FOS	chr1:172420340-172420537	MCF10A-Er-Src	breast:	n/a	chr1:172420447-172420455 chr1:172420445-172420456 chr1:172420445-172420457
36	JUND	chr1:172420261-172420578	HepG2	liver:	n/a	chr1:172420447-172420455 chr1:172420445-172420456 chr1:172420445-172420457
37	JUND	chr1:172420084-172420745	MCF-7	breast:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420445-172420456 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
38	MAZ	chr1:172418831-172420595	HepG2	liver:	n/a	chr1:172420446-172420455
39	CHD2	chr1:172420164-172420579	Hela-S3	cervix:	n/a	n/a
40	MYBL2	chr1:172420160-172420711	HepG2	liver:	n/a	n/a
41	NR2F2	chr1:172419483-172420685	MCF-7	breast:	n/a	n/a
42	CBX3	chr1:172419982-172420608	K562	blood:	n/a	n/a
43	JUN	chr1:172420321-172420595	HepG2	liver:	n/a	chr1:172420447-172420455 chr1:172420445-172420457
44	FOSL1	chr1:172420331-172420531	K562	blood:	n/a	chr1:172420447-172420455 chr1:172420445-172420457 chr1:172420445-172420456
45	MAFF	chr1:172420355-172420560	K562	blood:	n/a	n/a
46	CTCF	chr1:172417456-172420817	A549	lung:	n/a	chr1:172419229-172419247 chr1:172420251-172420259 chr1:172419777-172419790 chr1:172419234-172419242 chr1:172419231-172419252
47	JUND	chr1:172420187-172420596	A549	lung:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420445-172420456 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
48	ZNF217	chr1:172419800-172420593	MCF-7	breast:	n/a	n/a
49	FOSL2	chr1:172420061-172420685	MCF-7	breast:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
50	FOSL2	chr1:172420040-172420683	MCF-7	breast:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234

No.	Distal block	Cell Line	Cell type
1	chr1:172419256..172421468-chr1:172500783..172504604,4	K562	blood:
2	chr1:172416845..172420491-chr1:172421660..172424212,3	MCF-7	breast:
3	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
4	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: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1063412	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10752946	0.95[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs10752957	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs10798005	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs11484605	0.83[ASN][1000 genomes]
rs13932	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894634	0.82[EUR][1000 genomes]
rs2097500	0.82[EUR][1000 genomes]
rs2157450	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs2213740	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs2269613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269615	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2269616	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2285170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2285171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285172	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285173	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285176	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2301455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2422141	0.83[ASN][1000 genomes]
rs2901656	0.81[CHB][hapmap]
rs3213563	0.95[ASN][1000 genomes]
rs3937046	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916186	0.82[ASN][1000 genomes]
rs4916258	0.95[ASN][1000 genomes]
rs60302909	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60821093	0.80[EUR][1000 genomes]
rs6424923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6658843	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs6669286	0.86[EUR][1000 genomes]
rs6674073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680035	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6689377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690191	0.86[EUR][1000 genomes]
rs6692458	0.82[CEU][hapmap]
rs6695139	0.82[CEU][hapmap]
rs6699095	0.81[CHB][hapmap]
rs6702667	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs7411767	0.83[ASN][1000 genomes]
rs7516301	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs7550016	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs9286858	0.94[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs929098	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425308	0.90[CHB][hapmap];0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs9425311	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs9425313	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9425316	0.82[ASN][1000 genomes]
rs9425329	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9425334	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9425598	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs9425600	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs9425601	0.81[ASN][1000 genomes]
rs9425602	0.80[ASN][1000 genomes]
rs9425604	0.80[ASN][1000 genomes]
rs9425606	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs9425619	0.86[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

No data

Chromatin state (count:62 , 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	chr1:172416400-172420600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172416400-172420600	Enhancers	HMEC	breast
5	chr1:172417200-172420600	Enhancers	NHEK	skin
6	chr1:172417200-172421800	Weak transcription	Psoas Muscle	Psoas
7	chr1:172417200-172423200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr1:172417600-172420800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:172417800-172420600	Enhancers	Placenta	Placenta
10	chr1:172417800-172420600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:172417800-172420800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:172417800-172420800	Enhancers	Fetal Kidney	kidney
13	chr1:172418000-172420800	Enhancers	HUVEC	blood vessel
14	chr1:172418000-172422200	Enhancers	NH-A	brain
15	chr1:172418400-172420600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:172418800-172420600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr1:172419000-172420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:172419000-172420600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:172419000-172420600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:172419000-172420600	Enhancers	Liver	Liver
21	chr1:172419000-172420600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:172419000-172420600	Enhancers	NHLF	lung
23	chr1:172419200-172420600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:172419200-172420800	Enhancers	Fetal Heart	heart
25	chr1:172419200-172420800	Enhancers	Osteobl	bone
26	chr1:172419400-172420600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:172419400-172420600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:172419400-172422200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:172419600-172420600	Enhancers	Primary T cells from cord blood	blood
30	chr1:172419600-172421400	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:172419600-172421600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:172419600-172422000	Weak transcription	Right Ventricle	heart
33	chr1:172419600-172423200	Enhancers	K562	blood
34	chr1:172419600-172426000	Enhancers	Fetal Intestine Large	intestine
35	chr1:172419800-172420600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:172419800-172420600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:172419800-172421400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:172419800-172421400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:172419800-172421400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:172419800-172424400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:172420000-172420600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:172420000-172420800	Flanking Active TSS	HepG2	liver
43	chr1:172420000-172421600	Weak transcription	Gastric	stomach
44	chr1:172420000-172421800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:172420200-172420800	Enhancers	A549	lung
46	chr1:172420200-172421600	Weak transcription	Right Atrium	heart
47	chr1:172420200-172426000	Enhancers	Fetal Intestine Small	intestine
48	chr1:172420400-172421400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:172420400-172421400	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:172420400-172421400	Weak transcription	Stomach Mucosa	stomach

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