Variant report

Variant	rs343992
Chromosome Location	chr3:156530170-156530171
allele	A/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	ZNF217	chr3:156530147-156530872	MCF-7	breast:	n/a	n/a
2	JUND	chr3:156530120-156530919	MCF-7	breast:	n/a	n/a
3	MAX	chr3:156530136-156530895	HCT-116	colon:	n/a	n/a
4	MYC	chr3:156530128-156530803	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF12	chr3:156530065-156531086	MCF-7	breast:	n/a	n/a
6	EP300	chr3:156529992-156531100	A549	lung:	n/a	chr3:156530503-156530511
7	SIN3AK20	chr3:156530141-156531109	MCF-7	breast:	n/a	n/a
8	CEBPB	chr3:156530077-156530853	HCT-116	colon:	n/a	chr3:156530291-156530304
9	TEAD4	chr3:156530152-156530860	K562	blood:	n/a	n/a
10	CEBPB	chr3:156530112-156530967	MCF-7	breast:	n/a	chr3:156530291-156530304
11	FOXM1	chr3:156530115-156531206	MCF-7	breast:	n/a	n/a
12	FOXM1	chr3:156530118-156530822	MCF-7	breast:	n/a	n/a
13	ARID3A	chr3:156530163-156530760	K562	blood:	n/a	n/a
14	EP300	chr3:156530040-156530927	A549	lung:	n/a	chr3:156530503-156530511
15	FOSL2	chr3:156530138-156530898	MCF-7	breast:	n/a	n/a
16	REST	chr3:156530149-156530998	A549	lung:	n/a	n/a
17	MYBL2	chr3:156530114-156530732	HepG2	liver:	n/a	n/a
18	EP300	chr3:156530006-156531006	MCF-7	breast:	n/a	chr3:156530503-156530511
19	MAX	chr3:156530134-156530895	A549	lung:	n/a	n/a
20	HDAC2	chr3:156530146-156531044	MCF-7	breast:	n/a	chr3:156530540-156530554 chr3:156530772-156530786
21	NR2F2	chr3:156530038-156531039	MCF-7	breast:	n/a	n/a
22	GATA3	chr3:156529904-156531158	MCF-7	breast:	n/a	chr3:156530611-156530618 chr3:156530862-156530874
23	MAX	chr3:156530070-156530938	A549	lung:	n/a	n/a
24	GATA3	chr3:156529997-156531219	MCF-7	breast:	n/a	chr3:156530611-156530618 chr3:156530862-156530874
25	MAX	chr3:156530126-156531387	MCF-7	breast:	n/a	n/a
26	ESR1	chr3:156530102-156530843	T-47D	breast:	n/a	chr3:156530445-156530460
27	TCF12	chr3:156530096-156531052	A549	lung:	n/a	n/a
28	EP300	chr3:156530168-156530949	Hela-S3	cervix:	n/a	chr3:156530503-156530511
29	TCF12	chr3:156529986-156530959	MCF-7	breast:	n/a	n/a
30	FOXA2	chr3:156529976-156530936	HepG2	liver:	n/a	n/a
31	CEBPB	chr3:156529986-156531016	HCT-116	colon:	n/a	chr3:156530291-156530304
32	SP1	chr3:156529973-156531017	A549	lung:	n/a	n/a
33	SP1	chr3:156530146-156531223	A549	lung:	n/a	n/a
34	NR2F2	chr3:156529996-156531220	MCF-7	breast:	n/a	n/a
35	CEBPB	chr3:156530125-156531014	A549	lung:	n/a	chr3:156530291-156530304
36	JUN	chr3:156530105-156531439	K562	blood:	n/a	chr3:156530498-156530511
37	GABPA	chr3:156530170-156530903	MCF-7	breast:	n/a	n/a
38	CEBPB	chr3:156530027-156530887	MCF-7	breast:	n/a	chr3:156530291-156530304
39	CEBPB	chr3:156530020-156530920	A549	lung:	n/a	chr3:156530291-156530304
40	BCL3	chr3:156530064-156530838	A549	lung:	n/a	n/a
41	TCF7L2	chr3:156530109-156530763	MCF-7	breast:	n/a	n/a
42	CEBPB	chr3:156530162-156530868	IMR90	lung:	n/a	chr3:156530291-156530304
43	CBX3	chr3:156530144-156530768	K562	blood:	n/a	n/a
44	GATA3	chr3:156529950-156531076	A549	lung:	n/a	chr3:156530611-156530618 chr3:156530862-156530874
45	CEBPB	chr3:156530134-156530879	K562	blood:	n/a	chr3:156530291-156530304
46	JUND	chr3:156530144-156530974	MCF-7	breast:	n/a	n/a
47	SIN3AK20	chr3:156529995-156530909	MCF-7	breast:	n/a	n/a
48	CEBPB	chr3:156530144-156530833	K562	blood:	n/a	chr3:156530291-156530304
49	CEBPB	chr3:156530130-156530824	HepG2	liver:	n/a	chr3:156530291-156530304
50	HDAC2	chr3:156530160-156530865	MCF-7	breast:	n/a	chr3:156530540-156530554 chr3:156530772-156530786

No.	Distal block	Cell Line	Cell type
1	chr3:156530048..156530904-chr3:156886285..156887118,3	MCF-7	breast:
2	chr3:156259874..156260775-chr3:156530012..156530938,9	MCF-7	breast:
3	chr3:156391501..156392504-chr3:156530032..156530895,8	MCF-7	breast:
4	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
5	chr3:156529964..156530922-chr3:156661054..156661859,3	MCF-7	breast:
6	chr3:153936302..153937164-chr3:156529968..156530669,2	MCF-7	breast:
7	chr3:156529223..156530794-chr3:156884048..156887029,2	MCF-7	breast:
8	chr3:156530062..156530904-chr3:156657813..156658529,2	MCF-7	breast:
9	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
10	chr3:156259842..156261109-chr3:156529984..156531073,17	MCF-7	breast:
11	chr3:156392358..156392889-chr3:156529912..156530516,2	MCF-7	breast:
12	chr3:156526016..156527840-chr3:156529413..156531973,3	MCF-7	breast:
13	chr3:156519269..156521582-chr3:156529523..156531726,2	K562	blood:
14	chr3:156529794..156532107-chr3:156865235..156867004,2	K562	blood:
15	chr3:150454813..150455567-chr3:156530003..156530875,3	MCF-7	breast:
16	chr3:156391620..156392380-chr3:156529947..156530786,2	MCF-7	breast:
17	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:
18	chr3:156407951..156412215-chr3:156529722..156531947,3	MCF-7	breast:
19	chr3:156355246..156356229-chr3:156530151..156531163,7	MCF-7	breast:
20	chr3:156355498..156356029-chr3:156530091..156530958,2	MCF-7	breast:
21	chr3:156391521..156392512-chr3:156530025..156531053,11	MCF-7	breast:
22	chr3:156355156..156356223-chr3:156530151..156531163,9	MCF-7	breast:
23	chr3:156260163..156261184-chr3:156530021..156530957,10	MCF-7	breast:

Variant related genes	Relation type
PA2G4P4	TF binding region
ENSG00000243926	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs11710516	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11717138	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11927500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13321802	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1355280	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1430412	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1510269	0.83[ASN][1000 genomes]
rs1510270	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16826858	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16826899	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16826906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16826948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs171077	0.94[ASN][1000 genomes]
rs171080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs180746	0.94[ASN][1000 genomes]
rs180747	1.00[CHB][hapmap]
rs182935	0.83[ASN][1000 genomes]
rs182936	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs184677	1.00[CHB][hapmap]
rs193198	1.00[CHB][hapmap]
rs193423	1.00[CHB][hapmap]
rs2054881	1.00[CHB][hapmap]
rs2129909	1.00[CHB][hapmap]
rs2163296	0.85[ASN][1000 genomes]
rs237246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2633815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2665390	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs28661978	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2874490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2874491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs344000	0.83[ASN][1000 genomes]
rs344001	0.83[ASN][1000 genomes]
rs344005	1.00[CHB][hapmap]
rs344006	1.00[CHB][hapmap]
rs344008	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs344009	1.00[CHB][hapmap]
rs344010	1.00[CHB][hapmap]
rs344011	1.00[CHB][hapmap]
rs344012	1.00[CHB][hapmap]
rs344013	1.00[CHB][hapmap]
rs344014	1.00[CHB][hapmap]
rs344015	1.00[CHB][hapmap]
rs344016	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs344017	1.00[CHB][hapmap]
rs344023	0.94[ASN][1000 genomes]
rs344032	0.89[ASN][1000 genomes]
rs344047	0.94[ASN][1000 genomes]
rs344048	0.94[ASN][1000 genomes]
rs344049	0.94[ASN][1000 genomes]
rs344050	0.94[ASN][1000 genomes]
rs344052	1.00[CHB][hapmap]
rs344053	1.00[CHB][hapmap]
rs344054	1.00[CHB][hapmap]
rs344055	1.00[CHB][hapmap]
rs344058	1.00[CHB][hapmap]
rs344059	1.00[CHB][hapmap]
rs344060	1.00[CHB][hapmap]
rs344061	1.00[CHB][hapmap]
rs344062	1.00[CHB][hapmap]
rs344063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344064	1.00[CHB][hapmap]
rs344065	1.00[CHB][hapmap]
rs344066	1.00[CHB][hapmap]
rs344068	1.00[CHB][hapmap]
rs344069	1.00[CHB][hapmap]
rs344070	1.00[CHB][hapmap]
rs344074	1.00[CHB][hapmap]
rs344076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs344077	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs344081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs344085	0.89[CEU][hapmap];0.83[CHD][hapmap];0.83[LWK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344088	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3796172	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs414683	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs419287	1.00[CHB][hapmap]
rs427384	1.00[CHB][hapmap]
rs4279048	0.83[ASN][1000 genomes]
rs4429586	1.00[CHB][hapmap]
rs4679784	0.83[ASN][1000 genomes]
rs4680298	0.83[CHD][hapmap]
rs4680299	0.83[CHD][hapmap]
rs4680304	0.95[ASN][1000 genomes]
rs491423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs59244547	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441092	0.83[CHD][hapmap]
rs6441095	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6441099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6441100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6441104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763644	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6786167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6787535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6787952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6792917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6795327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6795516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6799457	0.83[CHD][hapmap]
rs6802042	1.00[JPT][hapmap]
rs6802511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7609851	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7618306	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7621699	1.00[CEU][hapmap]
rs7630909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7635521	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7650127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs978108	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs978109	0.83[ASN][1000 genomes]
rs9823112	1.00[CHB][hapmap]
rs9847692	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9861359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9878709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:156520200-156530400	Weak transcription	Right Ventricle	heart
3	chr3:156522200-156530400	Weak transcription	Gastric	stomach
4	chr3:156526200-156530600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:156526400-156530600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:156527000-156530400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:156527200-156533200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:156527400-156531600	Enhancers	Fetal Intestine Small	intestine
9	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:156527800-156533000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:156527800-156533800	Enhancers	HMEC	breast
12	chr3:156528200-156533600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:156528400-156530800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:156528400-156531000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:156528400-156531200	Enhancers	Fetal Intestine Large	intestine
16	chr3:156528400-156531200	Enhancers	HUVEC	blood vessel
17	chr3:156528400-156531200	Enhancers	NHDF-Ad	bronchial
18	chr3:156528400-156532800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:156528600-156531200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:156528600-156531200	Enhancers	HepG2	liver
21	chr3:156528800-156530200	Weak transcription	Lung	lung
22	chr3:156528800-156530400	Weak transcription	Esophagus	oesophagus
23	chr3:156528800-156531600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:156528800-156531600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:156529000-156530400	Weak transcription	Right Atrium	heart
26	chr3:156529000-156530400	Enhancers	Hela-S3	cervix
27	chr3:156529000-156530600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:156529000-156530600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:156529000-156530600	Weak transcription	Small Intestine	intestine
30	chr3:156529000-156531200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:156529000-156531200	Enhancers	Osteobl	bone
32	chr3:156529000-156531400	Enhancers	Liver	Liver
33	chr3:156529000-156531400	Enhancers	K562	blood
34	chr3:156529000-156531400	Enhancers	NH-A	brain
35	chr3:156529000-156531600	Enhancers	Primary T cells from cord blood	blood
36	chr3:156529200-156530800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:156529200-156531000	Enhancers	NHLF	lung
38	chr3:156529200-156531200	Enhancers	Stomach Mucosa	stomach
39	chr3:156529200-156533600	Weak transcription	Primary B cells from cord blood	blood
40	chr3:156529400-156530400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:156529400-156530400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:156529400-156531200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:156529400-156531400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:156529400-156533400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:156529600-156530400	Weak transcription	Psoas Muscle	Psoas
46	chr3:156529600-156530600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:156529600-156530600	Active TSS	GM12878-XiMat	blood
48	chr3:156529600-156530800	Weak transcription	Fetal Thymus	thymus
49	chr3:156529600-156531400	Flanking Active TSS	NHEK	skin
50	chr3:156529600-156532400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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