Variant report

Variant	rs55880223
Chromosome Location	chr14:39645265-39645266
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	chr14:39643825-39645302	GM12878	blood:	n/a	chr14:39644996-39645003
2	POLR2A	chr14:39645121-39645430	HUVEC	blood vessel:	n/a	n/a
3	WRNIP1	chr14:39643371-39645398	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:39643918-39645308	IMR90	lung:	n/a	n/a
5	REST	chr14:39643618-39645414	HepG2	liver:	n/a	chr14:39644625-39644638
6	POLR2A	chr14:39643127-39645394	K562	blood:	n/a	n/a
7	POLR2A	chr14:39643919-39645402	HepG2	liver:	n/a	n/a
8	POLR2A	chr14:39643132-39645483	GM12892	blood:	n/a	n/a
9	POLR2A	chr14:39643640-39645498	GM12892	blood:	n/a	n/a
10	CHD1	chr14:39643485-39645701	IMR90	lung:	n/a	chr14:39644663-39644673
11	POLR2A	chr14:39643741-39645327	HepG2	liver:	n/a	n/a
12	MAZ	chr14:39643838-39645269	K562	blood:	n/a	chr14:39644996-39645003
13	YY1	chr14:39643867-39645387	HepG2	liver:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
14	MXI1	chr14:39643829-39645457	IMR90	lung:	n/a	n/a
15	HDAC2	chr14:39643511-39645302	HepG2	liver:	n/a	chr14:39643628-39643642
16	CREB1	chr14:39643207-39645484	HepG2	liver:	n/a	n/a
17	MXI1	chr14:39643696-39645425	HepG2	liver:	n/a	n/a
18	GTF2F1	chr14:39644957-39645438	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr14:39643277-39645350	K562	blood:	n/a	chr14:39644996-39645003
20	CREB1	chr14:39643758-39645291	GM12878	blood:	n/a	n/a
21	MYBL2	chr14:39643054-39645503	HepG2	liver:	n/a	n/a
22	MAX	chr14:39643410-39645398	A549	lung:	n/a	chr14:39644996-39645003
23	POLR2A	chr14:39642960-39651251	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr14:39643183-39645441	H1-hESC	embryonic stem cell:	n/a	n/a
25	RCOR1	chr14:39643802-39645276	HepG2	liver:	n/a	n/a
26	POLR2A	chr14:39643160-39645412	GM12878	blood:	n/a	n/a
27	NFIC	chr14:39643501-39645806	HepG2	liver:	n/a	n/a
28	TBP	chr14:39643759-39645385	HepG2	liver:	n/a	n/a
29	POLR2A	chr14:39643065-39645495	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr14:39643729-39645337	K562	blood:	n/a	n/a
31	MYC	chr14:39643761-39645604	MCF10A-Er-Src	breast:	n/a	chr14:39644996-39645003
32	GABPA	chr14:39644726-39645347	HL-60	blood:	n/a	n/a
33	POLR2A	chr14:39643188-39645452	GM12891	blood:	n/a	n/a
34	POLR2A	chr14:39643289-39645298	GM18951	blood:	n/a	n/a
35	GABPA	chr14:39643875-39645435	HL-60	blood:	n/a	chr14:39643992-39644006 chr14:39643989-39644003 chr14:39644662-39644671 chr14:39643992-39644003
36	IRF1	chr14:39644966-39645432	K562	blood:	n/a	n/a
37	MYC	chr14:39643790-39645421	Hela-S3	cervix:	n/a	chr14:39644996-39645003
38	POLR2A	chr14:39643185-39645335	GM12892	blood:	n/a	n/a
39	HCFC1	chr14:39643954-39645361	K562	blood:	n/a	n/a
40	EP300	chr14:39643931-39645338	HepG2	liver:	n/a	chr14:39644123-39644131 chr14:39645102-39645116
41	POLR2A	chr14:39643760-39645433	PANC-1	pancreas:	n/a	n/a
42	CHD1	chr14:39643994-39645360	GM12878	blood:	n/a	chr14:39644663-39644673
43	ELF1	chr14:39643567-39645387	HepG2	liver:	n/a	chr14:39645101-39645112
44	GABPA	chr14:39643892-39645339	MCF-7	breast:	n/a	chr14:39643992-39644006 chr14:39643989-39644003 chr14:39644662-39644671 chr14:39643992-39644003
45	POLR2A	chr14:39643126-39645393	GM12892	blood:	n/a	n/a
46	HEY1	chr14:39643699-39645520	HepG2	liver:	n/a	chr14:39644415-39644430
47	MXI1	chr14:39644931-39645269	K562	blood:	n/a	n/a
48	ARID3A	chr14:39643431-39645626	HepG2	liver:	n/a	n/a
49	POLR2A	chr14:39643051-39648902	HepG2	liver:	n/a	n/a
50	MYC	chr14:39643780-39645336	MCF10A-Er-Src	breast:	n/a	chr14:39644996-39645003

No.	Distal block	Cell Line	Cell type
1	chr14:39643730..39648156-chr14:39734640..39738499,10	MCF-7	breast:
2	chr14:39642546..39647225-chr14:39733415..39737853,13	MCF-7	breast:
3	chr14:39643409..39646477-chr14:39682252..39685201,4	MCF-7	breast:
4	chr14:39582116..39585012-chr14:39643452..39645860,4	MCF-7	breast:
5	chr14:39642562..39645375-chr14:39698449..39701112,2	MCF-7	breast:
6	chr14:39644686..39646338-chr14:39899658..39902040,2	K562	blood:
7	chr14:39644463..39645283-chr2:24307157..24307928,2	Hela-S3	cervix:

Variant related genes	Relation type
PNN	TF binding region
ENSG00000259083	TF binding region
ENSG00000258941	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000092208	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000150526	Chromatin interaction
ENSG00000165355	Chromatin interaction
ENSG00000270503	Chromatin interaction
ENSG00000115129	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10483540	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108815	0.83[EUR][1000 genomes]
rs45469295	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45469795	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs45540035	0.89[EUR][1000 genomes]
rs55706043	1.00[ASN][1000 genomes]
rs55790340	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55918207	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55981737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987939	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997577	0.89[EUR][1000 genomes]
rs56032918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56063785	0.80[EUR][1000 genomes]
rs56074634	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56087094	0.80[EUR][1000 genomes]
rs56103446	0.89[EUR][1000 genomes]
rs56125789	0.89[EUR][1000 genomes]
rs56136756	0.80[EUR][1000 genomes]
rs56182546	1.00[ASN][1000 genomes]
rs56225465	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56225696	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs56237815	0.80[EUR][1000 genomes]
rs56276842	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56328886	0.80[EUR][1000 genomes]
rs56333870	0.87[EUR][1000 genomes]
rs56334607	0.80[EUR][1000 genomes]
rs56335002	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56341545	0.80[EUR][1000 genomes]
rs56404404	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57248532	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59418195	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6571907	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67808375	0.91[EUR][1000 genomes]
rs67970726	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147914	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148908	0.80[EUR][1000 genomes]
rs7150638	0.83[EUR][1000 genomes]
rs7161065	0.87[EUR][1000 genomes]
rs72671316	0.80[EUR][1000 genomes]
rs72671333	0.80[EUR][1000 genomes]
rs72671344	0.80[EUR][1000 genomes]
rs72671349	0.80[EUR][1000 genomes]
rs72671353	0.80[EUR][1000 genomes]
rs72671360	0.85[EUR][1000 genomes]
rs72671362	0.85[EUR][1000 genomes]
rs72671367	0.85[EUR][1000 genomes]
rs72671372	0.89[EUR][1000 genomes]
rs72671379	0.89[EUR][1000 genomes]
rs72671382	0.89[EUR][1000 genomes]
rs72671387	0.89[EUR][1000 genomes]
rs72671398	0.89[EUR][1000 genomes]
rs72671400	0.89[EUR][1000 genomes]
rs72673314	0.89[EUR][1000 genomes]
rs72673315	0.91[EUR][1000 genomes]
rs72673316	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72673317	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72673318	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72673328	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673329	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673339	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673340	0.93[EUR][1000 genomes]
rs72673346	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673350	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673357	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673358	0.82[AFR][1000 genomes]
rs72673359	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673379	1.00[ASN][1000 genomes]
rs72673381	1.00[ASN][1000 genomes]
rs72673384	1.00[ASN][1000 genomes]
rs72673387	1.00[ASN][1000 genomes]
rs72673388	1.00[ASN][1000 genomes]
rs8009457	0.80[EUR][1000 genomes]

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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39643200-39645600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:39643200-39645600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr14:39643400-39645400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:39643400-39645400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr14:39643400-39645600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr14:39643400-39645600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:39643400-39645600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr14:39643400-39645600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:39643400-39645600	Active TSS	Fetal Intestine Small	intestine
10	chr14:39643400-39645600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr14:39643400-39645800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr14:39643600-39645400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:39643600-39645400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:39643600-39645400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:39643600-39645400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:39643600-39645400	Active TSS	Muscle Satellite Cultured Cells	--
17	chr14:39643600-39645400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr14:39643600-39645400	Active TSS	Aorta	Aorta
19	chr14:39643600-39645400	Active TSS	Esophagus	oesophagus
20	chr14:39643600-39645400	Active TSS	Ovary	ovary
21	chr14:39643600-39645400	Active TSS	Pancreas	Pancrea
22	chr14:39643600-39645600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr14:39643600-39645600	Active TSS	HSMMtube	muscle
24	chr14:39643600-39645600	Active TSS	NHDF-Ad	bronchial
25	chr14:39643600-39645600	Active TSS	NHLF	lung
26	chr14:39643600-39645800	Active TSS	Fetal Brain Female	brain
27	chr14:39643600-39645800	Active TSS	Psoas Muscle	Psoas
28	chr14:39643600-39645800	Active TSS	Right Ventricle	heart
29	chr14:39643600-39645800	Active TSS	K562	blood
30	chr14:39643600-39646000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr14:39643600-39646000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr14:39643800-39645400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:39643800-39645400	Active TSS	Colonic Mucosa	Colon
34	chr14:39643800-39645400	Active TSS	Placenta	Placenta
35	chr14:39643800-39645400	Active TSS	Gastric	stomach
36	chr14:39643800-39645400	Active TSS	Left Ventricle	heart
37	chr14:39643800-39645400	Active TSS	Lung	lung
38	chr14:39643800-39645400	Active TSS	Placenta Amnion	Placenta Amnion
39	chr14:39643800-39645400	Active TSS	Stomach Mucosa	stomach
40	chr14:39643800-39645400	Active TSS	GM12878-XiMat	blood
41	chr14:39643800-39645400	Active TSS	Hela-S3	cervix
42	chr14:39643800-39645400	Active TSS	HUVEC	blood vessel
43	chr14:39643800-39645400	Active TSS	NHEK	skin
44	chr14:39643800-39645600	Active TSS	Liver	Liver
45	chr14:39643800-39645600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr14:39643800-39645600	Active TSS	Fetal Intestine Large	intestine
47	chr14:39643800-39645800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr14:39643800-39646000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr14:39643800-39646200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:39643800-39646600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links