Variant report

Variant	rs3742566
Chromosome Location	chr14:55595839-55595840
allele	A/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	MAZ	chr14:55595650-55596194	K562	blood:	n/a	chr14:55595693-55595703
2	YY1	chr14:55595821-55596117	GM12891	blood:	n/a	chr14:55595892-55595901 chr14:55595961-55595975 chr14:55595964-55595978
3	ZNF143	chr14:55595771-55596803	GM12878	blood:	n/a	chr14:55595965-55595975 chr14:55595841-55595851 chr14:55596519-55596537 chr14:55595920-55595938
4	JUND	chr14:55595691-55596150	A549	lung:	n/a	chr14:55595896-55595905
5	ZEB1	chr14:55595601-55596039	GM12878	blood:	n/a	n/a
6	CHD2	chr14:55595606-55597252	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr14:55595445-55597213	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr14:55595636-55597363	IMR90	lung:	n/a	n/a
9	MAZ	chr14:55595592-55596932	GM12878	blood:	n/a	chr14:55595693-55595703
10	CHD1	chr14:55595814-55596592	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:55595595-55596768	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3A	chr14:55595619-55595859	H1-hESC	embryonic stem cell:	n/a	n/a
13	HMGN3	chr14:55595620-55596717	K562	blood:	n/a	n/a
14	POLR2A	chr14:55595497-55597310	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr14:55595626-55596371	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr14:55595617-55596169	A549	lung:	n/a	n/a
17	RCOR1	chr14:55595603-55596177	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr14:55595820-55597085	IMR90	lung:	n/a	chr14:55596180-55596192 chr14:55596409-55596418
19	POLR2A	chr14:55595654-55596164	HUVEC	blood vessel:	n/a	n/a
20	RFX5	chr14:55595617-55596126	Hela-S3	cervix:	n/a	n/a
21	MAX	chr14:55595533-55597366	A549	lung:	n/a	chr14:55595693-55595703 chr14:55597040-55597049
22	POLR2A	chr14:55595591-55596843	MCF-7	breast:	n/a	n/a
23	HA-E2F1	chr14:55595609-55596266	Hela-S3	cervix:	n/a	chr14:55595960-55595969 chr14:55595841-55595850 chr14:55596179-55596188 chr14:55595818-55595828
24	TAF1	chr14:55595608-55596769	ECC-1	luminal epithelium:	n/a	n/a
25	MAZ	chr14:55595783-55595938	HepG2	liver:	n/a	n/a
26	E2F4	chr14:55595757-55596071	MCF10A-Er-Src	breast:	n/a	chr14:55595960-55595969 chr14:55595841-55595850 chr14:55595818-55595828
27	PML	chr14:55595603-55596275	MCF-7	breast:	n/a	n/a
28	MYC	chr14:55595838-55596033	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr14:55595650-55596103	K562	blood:	n/a	n/a
30	HEY1	chr14:55595756-55596172	HepG2	liver:	n/a	chr14:55595838-55595853 chr14:55595959-55595974 chr14:55595916-55595931 chr14:55595950-55595965
31	ELF1	chr14:55595551-55595946	GM12878	blood:	n/a	n/a
32	REST	chr14:55595760-55596404	MCF-7	breast:	n/a	chr14:55596253-55596261 chr14:55595865-55595878
33	POLR2A	chr14:55595591-55596243	HCT-116	colon:	n/a	n/a
34	CCNT2	chr14:55595664-55596443	K562	blood:	n/a	n/a
35	POLR2A	chr14:55595603-55596183	HCT-116	colon:	n/a	n/a
36	MAX	chr14:55595835-55596116	K562	blood:	n/a	n/a
37	HDAC2	chr14:55595619-55597303	MCF-7	breast:	n/a	chr14:55597268-55597277
38	POLR2A	chr14:55595626-55596860	GM12878	blood:	n/a	n/a
39	TCF7L2	chr14:55595749-55596679	HCT-116	colon:	n/a	n/a
40	GATA1	chr14:55595280-55596374	PBDE	blood:	n/a	chr14:55595404-55595420 chr14:55595430-55595439 chr14:55595409-55595426 chr14:55595432-55595439
41	TBP	chr14:55595802-55595984	HepG2	liver:	n/a	n/a
42	EP300	chr14:55595603-55596134	T-47D	breast:	n/a	chr14:55595966-55595975 chr14:55595841-55595850 chr14:55595819-55595828 chr14:55595962-55595978
43	ZBTB7A	chr14:55595558-55596073	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr14:55595665-55596912	GM12878	blood:	n/a	n/a
45	POLR2A	chr14:55595128-55597550	Hela-S3	cervix:	n/a	n/a
46	MAX	chr14:55595637-55597297	MCF-7	breast:	n/a	chr14:55595693-55595703 chr14:55597040-55597049
47	SMC3	chr14:55595672-55597277	Hela-S3	cervix:	n/a	chr14:55596339-55596349
48	POLR2A	chr14:55595086-55597263	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr14:55595626-55596762	GM18526	blood:	n/a	n/a
50	TCF7L2	chr14:55595721-55597199	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55368311..55371330-chr14:55594542..55598408,4	MCF-7	breast:
2	chr14:55516981..55523073-chr14:55594365..55600344,10	MCF-7	breast:
3	chr14:55595145..55596943-chr14:60714507..60716097,2	MCF-7	breast:
4	chr14:55595591..55597639-chr14:69257922..69259895,2	MCF-7	breast:
5	chr14:55492412..55494140-chr14:55594962..55596941,2	MCF-7	breast:
6	chr14:55518259..55522048-chr14:55593067..55596290,3	K562	blood:
7	chr14:55595164..55595992-chr16:87425741..87426276,2	Hela-S3	cervix:
8	chr14:55587248..55591020-chr14:55595215..55599629,4	K562	blood:
9	chr14:55517037..55520851-chr14:55594266..55601656,13	MCF-7	breast:
10	chr14:55595590..55596242-chrX:77359584..77360110,2	Hela-S3	cervix:
11	chr14:55594568..55597255-chr20:45984392..45987223,2	MCF-7	breast:

Variant related genes	Relation type
LGALS3	TF binding region
ENSG00000140941	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000180008	Chromatin interaction
ENSG00000103264	Chromatin interaction
ENSG00000198554	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000131979	Chromatin interaction
ENSG00000102144	Chromatin interaction
ENSG00000168175	Chromatin interaction
ENSG00000100614	Chromatin interaction
ENSG00000131981	Chromatin interaction
ENSG00000254718	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10137409	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10140857	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10149435	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10438127	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1047556	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11621351	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11622636	0.90[ASN][1000 genomes]
rs11622740	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs15870	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17253695	0.87[ASN][1000 genomes]
rs17672058	0.90[ASN][1000 genomes]
rs17832359	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1815316	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075603	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2094436	0.90[ASN][1000 genomes]
rs2147970	0.90[ASN][1000 genomes]
rs2147972	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2182207	0.98[ASN][1000 genomes]
rs2296489	0.93[ASN][1000 genomes]
rs2340936	0.88[ASN][1000 genomes]
rs3759667	0.90[ASN][1000 genomes]
rs3825613	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4040064	0.83[ASN][1000 genomes]
rs4525413	0.84[ASN][1000 genomes]
rs4644	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55710823	0.96[ASN][1000 genomes]
rs57033289	0.92[ASN][1000 genomes]
rs57970196	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58269011	0.83[ASN][1000 genomes]
rs66476033	0.90[ASN][1000 genomes]
rs66531545	0.93[ASN][1000 genomes]
rs66782529	0.96[ASN][1000 genomes]
rs66842809	0.90[ASN][1000 genomes]
rs66871576	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs67092614	0.90[ASN][1000 genomes]
rs67098772	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs67215571	0.90[ASN][1000 genomes]
rs67395212	0.98[ASN][1000 genomes]
rs67588230	0.90[ASN][1000 genomes]
rs67756714	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67805055	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs67958555	0.90[ASN][1000 genomes]
rs68083077	0.85[ASN][1000 genomes]
rs7140872	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72718804	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7493394	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55590800-55596200	Weak transcription	Fetal Lung	lung
2	chr14:55593000-55596400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr14:55593200-55597800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr14:55595200-55596200	Active TSS	Fetal Intestine Small	intestine
5	chr14:55595200-55596600	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr14:55595200-55596800	Active TSS	Fetal Intestine Large	intestine
7	chr14:55595200-55596800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr14:55595200-55596800	Active TSS	NH-A	brain
9	chr14:55595200-55598400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:55595400-55596200	Active TSS	GM12878-XiMat	blood
11	chr14:55595400-55596800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr14:55595400-55596800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:55595400-55596800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr14:55595400-55596800	Active TSS	Stomach Smooth Muscle	stomach
15	chr14:55595400-55597000	Active TSS	A549	lung
16	chr14:55595400-55597200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr14:55595400-55597200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr14:55595400-55597400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr14:55595400-55597400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr14:55595400-55597600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr14:55595400-55597600	Active TSS	NHDF-Ad	bronchial
22	chr14:55595400-55597800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr14:55595400-55606200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:55595600-55596000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr14:55595600-55596000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr14:55595600-55596000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr14:55595600-55596200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:55595600-55596200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr14:55595600-55596200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr14:55595600-55596200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr14:55595600-55596200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:55595600-55596200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr14:55595600-55596200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
34	chr14:55595600-55596200	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr14:55595600-55596200	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr14:55595600-55596400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr14:55595600-55596400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:55595600-55596400	Active TSS	Primary B cells from peripheral blood	blood
39	chr14:55595600-55596400	Active TSS	Placenta	Placenta
40	chr14:55595600-55596400	Active TSS	HUVEC	blood vessel
41	chr14:55595600-55596400	Active TSS	K562	blood
42	chr14:55595600-55596600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr14:55595600-55596600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr14:55595600-55596600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr14:55595600-55596600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr14:55595600-55596600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr14:55595600-55596600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:55595600-55596600	Active TSS	Adipose Nuclei	Adipose
49	chr14:55595600-55596600	Active TSS	Brain Cingulate Gyrus	brain
50	chr14:55595600-55596600	Active TSS	Brain Inferior Temporal Lobe	brain

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