Variant report

Variant	rs354302
Chromosome Location	chr5:14183866-14183867
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	MAX	chr5:14183748-14183948	A549	lung:	n/a	n/a
2	NR3C1	chr5:14183720-14183945	A549	lung:	n/a	n/a
3	POLR2A	chr5:14183610-14186820	U87	brain:	n/a	n/a
4	NR3C1	chr5:14183700-14184108	A549	lung:	n/a	n/a
5	POLR2A	chr5:14183654-14187699	PANC-1	pancreas:	n/a	n/a
6	NR3C1	chr5:14183713-14183948	A549	lung:	n/a	n/a
7	MYC	chr5:14183778-14183933	MCF10A-Er-Src	breast:	n/a	n/a
8	NR3C1	chr5:14183665-14184055	A549	lung:	n/a	n/a
9	MAX	chr5:14183577-14184074	A549	lung:	n/a	n/a
10	MYC	chr5:14183536-14184013	MCF10A-Er-Src	breast:	n/a	n/a
11	ZNF263	chr5:14181565-14185155	HEK293-T-REx	kidney:	n/a	chr5:14183654-14183663
12	NR3C1	chr5:14183673-14184002	A549	lung:	n/a	n/a
13	POLR2A	chr5:14183667-14186782	U87	brain:	n/a	n/a
14	POLR2A	chr5:14183819-14183941	A549	lung:	n/a	n/a
15	MAZ	chr5:14183640-14186934	IMR90	lung:	n/a	chr5:14185124-14185133 chr5:14185125-14185134
16	MAX	chr5:14183698-14184074	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14143107..14145345-chr5:14183034..14185852,4	MCF-7	breast:

Variant related genes	Relation type
TRIO	TF binding region
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13184670	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs151901	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs151902	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs164858	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs187386	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245447	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245448	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245451	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245470	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245512	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26057	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs26059	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26060	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26061	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs27665	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs27759	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28010	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32335	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs32339	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32341	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32388	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32389	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32390	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32391	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs32394	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32395	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs354298	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs354299	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs354300	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs354301	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs354310	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs354311	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs354312	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35594035	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs397098	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs407517	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs424275	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs445553	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs533517	1.00[EUR][1000 genomes]
rs56235530	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432716	chr5:13779700-14184600	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv516415	chr5:13788886-14210897	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1019196	chr5:13790760-14187503	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1018474	chr5:13798819-14184599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1024037	chr5:13798819-14185039	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv534466	chr5:13847044-14246208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	esv1830112	chr5:14147376-14222601	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv1792551	chr5:14180257-14202590	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14174400-14184400	Weak transcription	Colonic Mucosa	Colon
2	chr5:14174800-14184000	Weak transcription	Fetal Kidney	kidney
3	chr5:14175000-14184000	Weak transcription	Stomach Mucosa	stomach
4	chr5:14175000-14191600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:14175200-14186400	Weak transcription	Primary B cells from cord blood	blood
6	chr5:14177200-14189400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:14177400-14191800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:14178000-14184400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:14178600-14187000	Enhancers	Left Ventricle	heart
10	chr5:14178800-14184000	Enhancers	NH-A	brain
11	chr5:14179000-14184800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:14179200-14185400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:14179200-14189800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr5:14180400-14184400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:14180600-14185800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:14180800-14184200	Weak transcription	Hela-S3	cervix
17	chr5:14180800-14185400	Enhancers	HMEC	breast
18	chr5:14180800-14186800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:14181000-14187600	Enhancers	HUVEC	blood vessel
20	chr5:14181200-14189200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:14181400-14184000	Enhancers	GM12878-XiMat	blood
22	chr5:14181400-14186400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr5:14181400-14187600	Enhancers	Fetal Muscle Leg	muscle
24	chr5:14181400-14188600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr5:14181400-14189800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr5:14181400-14191800	Enhancers	Fetal Heart	heart
27	chr5:14181600-14186000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:14181600-14186200	Enhancers	HepG2	liver
29	chr5:14181600-14186400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr5:14181600-14189000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:14181800-14186600	Enhancers	Fetal Brain Female	brain
32	chr5:14182000-14185400	Weak transcription	Esophagus	oesophagus
33	chr5:14182000-14185600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:14182000-14185800	Weak transcription	Fetal Thymus	thymus
35	chr5:14182000-14190200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:14182200-14184400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:14182200-14187200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:14182400-14187200	Enhancers	Brain Anterior Caudate	brain
39	chr5:14182600-14185600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:14182600-14185800	Enhancers	Fetal Muscle Trunk	muscle
41	chr5:14182800-14186600	Enhancers	Fetal Stomach	stomach
42	chr5:14182800-14187600	Enhancers	Brain Hippocampus Middle	brain
43	chr5:14182800-14188600	Enhancers	Adipose Nuclei	Adipose
44	chr5:14183000-14184000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:14183000-14184000	Enhancers	Fetal Intestine Large	intestine
46	chr5:14183000-14184400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:14183000-14184600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:14183000-14184600	Enhancers	Liver	Liver
49	chr5:14183000-14184600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr5:14183000-14185800	Enhancers	H1 Cell Line	embryonic stem cell

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