Variant report

Variant	rs2287392
Chromosome Location	chr14:77767382-77767383
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	RAD21	chr14:77767263-77767794	HepG2	liver:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
2	SMC3	chr14:77767330-77767770	GM12878	blood:	n/a	chr14:77767365-77767372
3	RAD21	chr14:77767091-77767996	SK-N-SH	brain:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
4	RAD21	chr14:77767229-77767775	HepG2	liver:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
5	ZBTB7A	chr14:77767209-77767401	K562	blood:	n/a	n/a
6	CTCF	chr14:77767244-77767725	GM19238	blood:	n/a	chr14:77767343-77767351
7	BCL3	chr14:77767301-77767843	A549	lung:	n/a	n/a
8	FOXA2	chr14:77767284-77767808	A549	lung:	n/a	n/a
9	CTCF	chr14:77767133-77767725	K562	blood:	n/a	chr14:77767343-77767351
10	CTCF	chr14:77767297-77767703	H1-hESC	embryonic stem cell:	n/a	chr14:77767343-77767351
11	CTCF	chr14:77767137-77767858	MCF-7	breast:	n/a	chr14:77767343-77767351
12	CTCF	chr14:77767245-77767721	MCF-7	breast:	n/a	chr14:77767343-77767351
13	FOXA1	chr14:77767378-77767763	HepG2	liver:	n/a	n/a
14	CTCF	chr14:77767197-77767734	A549	lung:	n/a	chr14:77767343-77767351
15	CTCF	chr14:77767192-77767788	IMR90	lung:	n/a	chr14:77767343-77767351
16	CTCF	chr14:77767243-77767716	MCF-7	breast:	n/a	chr14:77767343-77767351
17	CTCF	chr14:77767152-77768001	SK-N-SH	brain:	n/a	chr14:77767343-77767351
18	CTCF	chr14:77767078-77768039	A549	lung:	n/a	chr14:77767343-77767351
19	CTCF	chr14:77767327-77767722	Spleen_OC	spleen:	n/a	chr14:77767343-77767351
20	FOXA1	chr14:77767369-77767804	T-47D	breast:	n/a	n/a
21	CTCF	chr14:77767288-77767395	GM20000	blood:	n/a	chr14:77767343-77767351
22	CTCF	chr14:77767310-77767693	LNCaP	prostate:	n/a	chr14:77767343-77767351
23	CTCF	chr14:77767132-77767760	K562	blood:	n/a	chr14:77767343-77767351
24	SMC3	chr14:77767364-77767777	HepG2	liver:	n/a	chr14:77767365-77767372
25	CTCF	chr14:77767248-77767707	MCF-7	breast:	n/a	chr14:77767343-77767351
26	CTCF	chr14:77767214-77767786	GM12878	blood:	n/a	chr14:77767343-77767351
27	CTCF	chr14:77767155-77767803	A549	lung:	n/a	chr14:77767343-77767351
28	CTCF	chr14:77767190-77767712	K562	blood:	n/a	chr14:77767343-77767351
29	NR2F2	chr14:77767224-77767834	MCF-7	breast:	n/a	n/a
30	CTCF	chr14:77767269-77767732	Medullo	brain:	n/a	chr14:77767343-77767351
31	CTCF	chr14:77767194-77767801	H1-hESC	embryonic stem cell:	n/a	chr14:77767343-77767351
32	CTCF	chr14:77767243-77767723	MCF-7	breast:	n/a	chr14:77767343-77767351
33	FOXA1	chr14:77767306-77767760	HepG2	liver:	n/a	n/a
34	CTCF	chr14:77767223-77767734	HepG2	liver:	n/a	chr14:77767343-77767351
35	CTCF	chr14:77767168-77767759	T-47D	breast:	n/a	chr14:77767343-77767351
36	CTCF	chr14:77767039-77767994	MCF-7	breast:	n/a	chr14:77767343-77767351
37	RAD21	chr14:77767245-77767706	SK-N-SH_RA	brain:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
38	RAD21	chr14:77767319-77767850	ECC-1	luminal epithelium:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
39	RAD21	chr14:77767182-77767922	MCF-7	breast:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
40	RAD21	chr14:77767300-77767747	H1-hESC	embryonic stem cell:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
41	RAD21	chr14:77767124-77767906	HCT-116	colon:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
42	KAP1	chr14:77767377-77768129	HEK293	kidney:	n/a	n/a
43	CTCF	chr14:77767199-77767706	HepG2	liver:	n/a	chr14:77767343-77767351
44	RAD21	chr14:77767210-77767772	HepG2	liver:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
45	SMC3	chr14:77767177-77767967	SK-N-SH	brain:	n/a	chr14:77767365-77767372
46	RAD21	chr14:77767164-77767887	A549	lung:	n/a	chr14:77767338-77767348 chr14:77767654-77767664 chr14:77767336-77767348
47	RAD21	chr14:77767351-77767814	H1-hESC	embryonic stem cell:	n/a	chr14:77767654-77767664
48	RAD21	chr14:77767353-77767781	A549	lung:	n/a	chr14:77767654-77767664
49	CTCF	chr14:77767154-77767895	HCT-116	colon:	n/a	chr14:77767343-77767351
50	CTCF	chr14:77767282-77767696	MCF-7	breast:	n/a	chr14:77767343-77767351

No.	Distal block	Cell Line	Cell type
1	chr14:77766406..77773210-chr14:77841892..77846481,6	MCF-7	breast:
2	chr14:77562016..77566150-chr14:77764439..77767879,4	MCF-7	breast:
3	chr14:77767197..77768126-chr14:77786720..77787641,3	MCF-7	breast:
4	chr14:77765577..77770355-chr14:77785292..77788769,6	K562	blood:

Variant related genes	Relation type
POMT2	TF binding region
ENSG00000198894	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000100580	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000259164	Chromatin interaction
ENSG00000100583	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10138030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1055592	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs11547793	0.87[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap]
rs11624564	0.95[CHD][hapmap];0.87[JPT][hapmap]
rs12437115	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17105672	0.84[CHD][hapmap]
rs2042045	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs2111699	0.82[JPT][hapmap]
rs2216089	0.81[CHD][hapmap]
rs2270422	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2287387	0.98[CHD][hapmap];0.82[JPT][hapmap]
rs2287388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2363638	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2363641	0.91[JPT][hapmap]
rs28374503	0.94[ASN][1000 genomes]
rs35149989	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs368855	0.82[MEX][hapmap]
rs3759733	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3783986	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs3783988	0.94[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs3783989	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3815626	0.91[JPT][hapmap]
rs4899650	0.95[JPT][hapmap]
rs4903567	0.98[CHD][hapmap];0.82[JPT][hapmap]
rs4903569	0.81[ASN][1000 genomes]
rs4903570	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6574367	0.91[JPT][hapmap]
rs6636	0.91[CHB][hapmap]
rs6637	0.83[CHB][hapmap]
rs71413458	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7142812	0.91[JPT][hapmap]
rs7158951	0.95[CHD][hapmap];0.87[JPT][hapmap]
rs7159558	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs731346	0.81[CHB][hapmap]
rs8009261	0.95[CHD][hapmap];0.87[JPT][hapmap]
rs8009733	0.95[CHD][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv902105	chr14:77764884-77801431	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2287392	C14orf156	cis	cerebellum	SCAN
rs2287392	GSTZ1	cis	lymphoblastoid	seeQTL
rs2287392	POMT2	cis	parietal	SCAN
rs2287392	EIF2B2	cis	cerebellum	SCAN
rs2287392	AHSA1	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
3	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
5	chr14:77742200-77767600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr14:77742400-77780200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:77744000-77771400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr14:77750200-77767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:77750800-77768000	Weak transcription	K562	blood
10	chr14:77751400-77769200	Weak transcription	NHLF	lung
11	chr14:77751400-77769800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr14:77751400-77775600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:77751400-77786200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr14:77751800-77767600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:77751800-77775600	Weak transcription	Thymus	Thymus
16	chr14:77752200-77775600	Weak transcription	Fetal Thymus	thymus
17	chr14:77752600-77773000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr14:77752600-77779200	Weak transcription	Fetal Heart	heart
19	chr14:77753600-77771800	Weak transcription	Fetal Brain Male	brain
20	chr14:77754600-77769200	Weak transcription	NHDF-Ad	bronchial
21	chr14:77754600-77771000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr14:77757600-77767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:77758400-77767800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:77759400-77767600	Weak transcription	Psoas Muscle	Psoas
25	chr14:77760400-77773000	Strong transcription	Fetal Stomach	stomach
26	chr14:77761200-77767800	Strong transcription	Lung	lung
27	chr14:77761400-77767600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr14:77761400-77767600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:77761400-77769200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:77761400-77769600	Strong transcription	Aorta	Aorta
31	chr14:77761600-77768400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:77762000-77767600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:77762000-77767600	Strong transcription	Left Ventricle	heart
34	chr14:77762200-77769200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr14:77762600-77767800	Weak transcription	HepG2	liver
36	chr14:77762600-77772400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:77762800-77767400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr14:77762800-77772200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr14:77762800-77774800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:77763400-77767600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:77763400-77771200	Weak transcription	Primary B cells from cord blood	blood
42	chr14:77763600-77769000	Weak transcription	Osteobl	bone
43	chr14:77764000-77770000	Weak transcription	Fetal Kidney	kidney
44	chr14:77764800-77769200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:77764800-77769800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr14:77765000-77767600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr14:77765000-77772000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:77765200-77767600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr14:77765200-77767600	Weak transcription	Right Atrium	heart
50	chr14:77765200-77768000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links