Variant report

Variant	rs354300
Chromosome Location	chr5:14184079-14184080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	1.00[CHB][hapmap]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151901	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151902	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164858	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299045	1.00[CHB][hapmap]
rs17299506	1.00[ASN][1000 genomes]
rs17302408	1.00[CHB][hapmap]
rs187125	1.00[CHB][hapmap]
rs187386	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap]
rs245447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245448	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245451	0.97[EUR][1000 genomes]
rs245470	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245512	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26058	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs26059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26060	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27759	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30616	1.00[CHB][hapmap]
rs30617	1.00[CHB][hapmap]
rs30619	1.00[CHB][hapmap]
rs30620	1.00[CHB][hapmap]
rs32335	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32388	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32389	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32391	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32395	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354285	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs354287	0.83[ASN][1000 genomes]
rs354288	1.00[ASN][1000 genomes]
rs354298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354299	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354301	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354302	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs354305	1.00[CHB][hapmap]
rs354310	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354311	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35594035	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849082	1.00[CHB][hapmap]
rs397098	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39856	1.00[CHB][hapmap]
rs407517	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424275	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs445553	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs533517	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235530	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706271	1.00[CHB][hapmap]
rs773701	1.00[CHB][hapmap]
rs773702	1.00[CHB][hapmap]
rs773703	1.00[CHB][hapmap]
rs773763	1.00[CHB][hapmap]
rs923616	1.00[CHB][hapmap]

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:104 , 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	chr5:14175000-14191600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:14175200-14186400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:14177200-14189400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:14177400-14191800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:14178000-14184400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:14178600-14187000	Enhancers	Left Ventricle	heart
8	chr5:14179000-14184800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:14179200-14185400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:14179200-14189800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr5:14180400-14184400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:14180600-14185800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:14180800-14184200	Weak transcription	Hela-S3	cervix
14	chr5:14180800-14185400	Enhancers	HMEC	breast
15	chr5:14180800-14186800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:14181000-14187600	Enhancers	HUVEC	blood vessel
17	chr5:14181200-14189200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:14181400-14186400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:14181400-14187600	Enhancers	Fetal Muscle Leg	muscle
20	chr5:14181400-14188600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr5:14181400-14189800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr5:14181400-14191800	Enhancers	Fetal Heart	heart
23	chr5:14181600-14186000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr5:14181600-14186200	Enhancers	HepG2	liver
25	chr5:14181600-14186400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:14181600-14189000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:14181800-14186600	Enhancers	Fetal Brain Female	brain
28	chr5:14182000-14185400	Weak transcription	Esophagus	oesophagus
29	chr5:14182000-14185600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr5:14182000-14185800	Weak transcription	Fetal Thymus	thymus
31	chr5:14182000-14190200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:14182200-14184400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:14182200-14187200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:14182400-14187200	Enhancers	Brain Anterior Caudate	brain
35	chr5:14182600-14185600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:14182600-14185800	Enhancers	Fetal Muscle Trunk	muscle
37	chr5:14182800-14186600	Enhancers	Fetal Stomach	stomach
38	chr5:14182800-14187600	Enhancers	Brain Hippocampus Middle	brain
39	chr5:14182800-14188600	Enhancers	Adipose Nuclei	Adipose
40	chr5:14183000-14184400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:14183000-14184600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:14183000-14184600	Enhancers	Liver	Liver
43	chr5:14183000-14184600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr5:14183000-14185800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr5:14183000-14185800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:14183000-14185800	Enhancers	Lung	lung
47	chr5:14183000-14186000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:14183000-14186200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:14183000-14186600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr5:14183000-14186600	Enhancers	Placenta	Placenta

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