Variant report

Variant	rs72911552
Chromosome Location	chr1:59280678-59280679
allele	C/G
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	TCF12	chr1:59280470-59282632	A549	lung:	n/a	chr1:59281207-59281217 chr1:59281032-59281041
2	POLR2A	chr1:59280614-59283094	U87	brain:	n/a	n/a
3	HMGN3	chr1:59280327-59281340	K562	blood:	n/a	n/a
4	MAX	chr1:59280519-59280785	K562	blood:	n/a	n/a
5	SRF	chr1:59280593-59281338	ECC-1	luminal epithelium:	n/a	chr1:59280998-59281013 chr1:59280970-59280980
6	SIN3A	chr1:59280238-59280967	H1-hESC	embryonic stem cell:	n/a	chr1:59280669-59280678
7	POLR2A	chr1:59279717-59282573	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:59280152-59281691	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr1:59280535-59282521	A549	lung:	n/a	chr1:59281157-59281167 chr1:59281157-59281167 chr1:59281098-59281112 chr1:59281163-59281177
10	ZNF143	chr1:59280590-59282283	Hela-S3	cervix:	n/a	chr1:59281084-59281094 chr1:59281914-59281924
11	CEBPB	chr1:59279686-59282432	Hela-S3	cervix:	n/a	chr1:59279976-59279987 chr1:59279927-59279935
12	TCF7L2	chr1:59280126-59282415	HCT-116	colon:	n/a	n/a
13	RCOR1	chr1:59280659-59282223	K562	blood:	n/a	n/a
14	MAX	chr1:59280425-59282538	A549	lung:	n/a	chr1:59281189-59281198
15	TCF12	chr1:59279676-59282551	ECC-1	luminal epithelium:	n/a	chr1:59281207-59281217 chr1:59281032-59281041
16	EGR1	chr1:59280327-59281316	ECC-1	luminal epithelium:	n/a	chr1:59280835-59280857 chr1:59281051-59281065 chr1:59281097-59281110 chr1:59280839-59280852 chr1:59280831-59280844 chr1:59280838-59280853 chr1:59280839-59280853 chr1:59280839-59280852
17	MYC	chr1:59280593-59280711	Hela-S3	cervix:	n/a	n/a
18	KAP1	chr1:59280626-59281969	HEK293	kidney:	n/a	n/a
19	EP300	chr1:59279720-59282623	ECC-1	luminal epithelium:	n/a	chr1:59281072-59281088 chr1:59282103-59282112 chr1:59281081-59281097 chr1:59282141-59282150 chr1:59281085-59281101 chr1:59281078-59281094 chr1:59281084-59281100 chr1:59281914-59281923
20	POLR2A	chr1:59280582-59282450	GM18951	blood:	n/a	n/a
21	ELK4	chr1:59280077-59282480	Hela-S3	cervix:	n/a	n/a
22	SMARCB1	chr1:59279838-59282407	Hela-S3	cervix:	n/a	n/a
23	TCF7L2	chr1:59280634-59281563	PANC-1	pancreas:	n/a	n/a
24	CHD2	chr1:59280405-59281101	H1-hESC	embryonic stem cell:	n/a	chr1:59280484-59280491
25	GTF2F1	chr1:59280314-59282488	Hela-S3	cervix:	n/a	n/a
26	FOXA2	chr1:59280590-59281328	A549	lung:	n/a	n/a
27	GATA3	chr1:59280568-59281286	T-47D	breast:	n/a	n/a
28	MAZ	chr1:59279861-59282340	Hela-S3	cervix:	n/a	chr1:59281189-59281198 chr1:59280253-59280262
29	NR2F2	chr1:59280464-59282561	K562	blood:	n/a	n/a
30	EGR1	chr1:59279749-59282500	HCT-116	colon:	n/a	chr1:59280835-59280857 chr1:59280060-59280074 chr1:59281051-59281065 chr1:59280060-59280073 chr1:59281909-59281922 chr1:59280063-59280072 chr1:59281097-59281110 chr1:59282140-59282149 chr1:59280839-59280852 chr1:59280831-59280844 chr1:59280838-59280853 chr1:59280839-59280853 chr1:59280059-59280074 chr1:59280061-59280072 chr1:59280839-59280852
31	ZBTB7A	chr1:59279846-59281372	ECC-1	luminal epithelium:	n/a	n/a
32	MAX	chr1:59280617-59282327	K562	blood:	n/a	chr1:59281189-59281198
33	CHD2	chr1:59280219-59282537	Hela-S3	cervix:	n/a	chr1:59281098-59281108 chr1:59280484-59280491
34	NR2F2	chr1:59280606-59281342	MCF-7	breast:	n/a	n/a
35	POLR2A	chr1:59279375-59282505	Hela-S3	cervix:	n/a	n/a
36	SIN3AK20	chr1:59279382-59282566	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:59280004-59281638	MCF-7	breast:	n/a	n/a
38	GATA3	chr1:59280501-59281335	MCF-7	breast:	n/a	n/a
39	ELF1	chr1:59279700-59281342	MCF-7	breast:	n/a	chr1:59280132-59280144 chr1:59280462-59280474 chr1:59280297-59280306
40	SP1	chr1:59280547-59282446	A549	lung:	n/a	chr1:59281157-59281167 chr1:59281157-59281167 chr1:59281098-59281112 chr1:59281163-59281177
41	TEAD4	chr1:59280149-59282391	ECC-1	luminal epithelium:	n/a	n/a
42	TCF12	chr1:59280281-59281404	MCF-7	breast:	n/a	chr1:59281207-59281217 chr1:59281032-59281041
43	FOXA1	chr1:59280677-59281226	ECC-1	luminal epithelium:	n/a	chr1:59281030-59281045
44	ELF1	chr1:59279859-59282614	HCT-116	colon:	n/a	chr1:59280132-59280144 chr1:59280462-59280474 chr1:59282105-59282114 chr1:59280297-59280306
45	RCOR1	chr1:59280612-59282375	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:59280530-59280745	H1-hESC	embryonic stem cell:	n/a	n/a
47	SMC3	chr1:59279900-59282839	Hela-S3	cervix:	n/a	n/a
48	EGR1	chr1:59280500-59281224	MCF-7	breast:	n/a	chr1:59280835-59280857 chr1:59281051-59281065 chr1:59281097-59281110 chr1:59280839-59280852 chr1:59280831-59280844 chr1:59280838-59280853 chr1:59280839-59280853 chr1:59280839-59280852
49	FOXM1	chr1:59280268-59281407	ECC-1	luminal epithelium:	n/a	n/a
50	USF2	chr1:59280478-59281971	Hela-S3	cervix:	n/a	chr1:59281085-59281101

No.	Distal block	Cell Line	Cell type
1	chr1:59279129..59280859-chr1:59347455..59349368,2	K562	blood:
2	chr1:59279353..59283854-chr1:59287313..59291525,6	MCF-7	breast:
3	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
4	chr1:59280122..59283663-chr1:59349956..59353437,4	K562	blood:
5	chr1:59279109..59280911-chr1:59291721..59294413,2	MCF-7	breast:
6	chr1:59280570..59282540-chr1:59362255..59364543,2	MCF-7	breast:
7	chr1:59243405..59253875-chr1:59275011..59289058,45	MCF-7	breast:
8	chr1:59279369..59282052-chr1:60171210..60173225,3	MCF-7	breast:
9	chr1:59279457..59282981-chr1:59283687..59286487,4	K562	blood:
10	chr1:59280503..59282768-chr1:59285490..59288010,2	MCF-7	breast:
11	chr1:59279471..59282455-chr1:59331094..59333680,2	MCF-7	breast:
12	chr1:59243458..59255133-chr1:59272031..59283720,29	K562	blood:
13	chr1:59279921..59284497-chr1:59286325..59289409,4	K562	blood:
14	chr1:59280334..59283471-chr1:59294258..59298511,4	K562	blood:
15	chr1:59280123..59281954-chr1:59395680..59397207,2	MCF-7	breast:
16	chr1:59279289..59281587-chr1:59349571..59351279,3	MCF-7	breast:
17	chr1:59279591..59281416-chr1:59282634..59284464,2	MCF-7	breast:
18	chr1:59279917..59282789-chr1:59295281..59296950,2	MCF-7	breast:
19	chr1:59091520..59094170-chr1:59279490..59282356,2	MCF-7	breast:
20	chr1:59280214..59283774-chr1:59346159..59349299,3	MCF-7	breast:
21	chr1:59280191..59282299-chr1:59284813..59286664,3	MCF-7	breast:
22	chr1:59279498..59283509-chr1:59392349..59395635,3	MCF-7	breast:
23	chr1:59279403..59281685-chr1:59758871..59761962,3	MCF-7	breast:
24	chr1:59279897..59281493-chr1:59891498..59894143,2	MCF-7	breast:
25	chr1:59279066..59281717-chr1:59892952..59895957,3	MCF-7	breast:
26	chr1:59279690..59282444-chr1:59408342..59410197,2	K562	blood:
27	chr1:59279994..59282679-chr1:59483503..59486905,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272226	TF binding region
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction
ENSG00000232453	Chromatin interaction
ENSG00000230812	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs3885883	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047424	1.00[EUR][1000 genomes]
rs57500803	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59164731	1.00[EUR][1000 genomes]
rs59193866	1.00[EUR][1000 genomes]
rs59558908	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60869213	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61294750	1.00[EUR][1000 genomes]
rs61659376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911524	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911526	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911533	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911535	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911538	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911540	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911542	1.00[ASN][1000 genomes]
rs72911543	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911546	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911559	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72913573	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72913576	1.00[EUR][1000 genomes]
rs72913582	1.00[EUR][1000 genomes]
rs72913585	1.00[EUR][1000 genomes]
rs72913586	1.00[EUR][1000 genomes]
rs72913589	1.00[EUR][1000 genomes]
rs72913594	1.00[EUR][1000 genomes]
rs72913595	1.00[EUR][1000 genomes]
rs72913598	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72913599	1.00[EUR][1000 genomes]
rs72913601	1.00[EUR][1000 genomes]
rs72915503	1.00[EUR][1000 genomes]
rs72915504	1.00[EUR][1000 genomes]
rs72915505	1.00[EUR][1000 genomes]
rs72915506	1.00[EUR][1000 genomes]
rs72915521	1.00[EUR][1000 genomes]
rs72915522	1.00[EUR][1000 genomes]
rs72915524	1.00[EUR][1000 genomes]
rs72915527	1.00[EUR][1000 genomes]
rs72919563	1.00[EUR][1000 genomes]
rs72919564	1.00[EUR][1000 genomes]
rs72919573	1.00[EUR][1000 genomes]
rs72919582	1.00[EUR][1000 genomes]
rs72919585	1.00[EUR][1000 genomes]
rs72919586	1.00[EUR][1000 genomes]
rs7519169	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59254000-59281000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:59274600-59281400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:59275400-59280800	Weak transcription	Fetal Heart	heart
4	chr1:59277600-59281200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:59277800-59280800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:59277800-59280800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:59277800-59281000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:59278000-59280800	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:59278000-59280800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:59278000-59281000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:59278200-59280800	Enhancers	Primary T cells from cord blood	blood
12	chr1:59278200-59280800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:59278200-59280800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:59278200-59281000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:59278200-59281000	Enhancers	Spleen	Spleen
16	chr1:59278400-59280800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr1:59278600-59281000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:59278800-59280800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:59278800-59281200	Enhancers	Gastric	stomach
20	chr1:59279000-59281200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:59279200-59280800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:59279200-59280800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:59279400-59281600	Flanking Active TSS	Hela-S3	cervix
24	chr1:59279600-59281800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:59279800-59281000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:59279800-59281400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:59279800-59281600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr1:59279800-59282400	Flanking Active TSS	HMEC	breast
29	chr1:59279800-59283400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:59280000-59280800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:59280000-59281000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr1:59280000-59281000	Bivalent Enhancer	Fetal Thymus	thymus
33	chr1:59280000-59281200	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr1:59280000-59281200	Weak transcription	Small Intestine	intestine
35	chr1:59280000-59281400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:59280000-59281600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:59280000-59281600	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr1:59280000-59281800	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr1:59280000-59281800	Flanking Active TSS	Fetal Stomach	stomach
40	chr1:59280000-59282000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:59280000-59282400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:59280000-59282600	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:59280000-59282600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:59280000-59282600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
45	chr1:59280000-59282600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr1:59280000-59282600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:59280200-59280800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:59280200-59280800	Flanking Active TSS	Placenta	Placenta
49	chr1:59280200-59280800	Flanking Active TSS	Right Atrium	heart
50	chr1:59280200-59280800	Flanking Active TSS	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links