Variant report

Variant	rs164109
Chromosome Location	chr5:14175415-14175416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14147506..14150169-chr5:14174482..14176062,2	MCF-7	breast:
2	chr5:14167574..14170191-chr5:14172276..14175858,4	MCF-7	breast:
3	chr5:14172374..14175679-chr5:14185951..14189494,3	MCF-7	breast:
4	chr5:14165692..14168086-chr5:14174628..14177292,2	MCF-7	breast:
5	chr5:14175254..14177607-chr5:14178876..14181098,2	MCF-7	breast:
6	chr5:14141856..14145674-chr5:14173554..14176741,3	MCF-7	breast:
7	chr5:14170364..14173641-chr5:14174629..14176326,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12652543	0.95[ASN][1000 genomes]
rs151899	0.86[JPT][hapmap]
rs152782	0.81[JPT][hapmap]
rs153191	0.83[MEX][hapmap]
rs164351	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs164521	0.81[AMR][1000 genomes]
rs164629	0.81[JPT][hapmap]
rs16903264	0.84[JPT][hapmap]
rs26281	0.82[JPT][hapmap]
rs26284	0.81[JPT][hapmap]
rs26285	0.81[JPT][hapmap]
rs26290	0.81[YRI][hapmap]
rs26292	0.81[YRI][hapmap]
rs27367	0.81[YRI][hapmap]
rs27482	0.84[JPT][hapmap]
rs27632	0.84[YRI][hapmap]
rs28014	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs32549	0.81[JPT][hapmap]
rs32571	0.95[JPT][hapmap]
rs32572	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32573	0.82[AMR][1000 genomes]
rs32594	0.81[JPT][hapmap]
rs33028	0.81[YRI][hapmap]
rs33030	0.84[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1020626	chr5:13798819-14177235	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1015479	chr5:13798819-14180804	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	esv2760949	chr5:13798819-14182550	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1017356	chr5:13798819-14182550	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv1030787	chr5:13799381-14180804	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1018784	chr5:13815834-14178505	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
12	nsv537672	chr5:13815834-14178505	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
13	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
14	nsv1020258	chr5:13849471-14178505	Genic enhancers Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
15	nsv537674	chr5:13849471-14178505	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
16	esv2752061	chr5:14109455-14178040	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
17	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
18	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
19	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
20	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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14164600-14181600	Weak transcription	Esophagus	oesophagus
2	chr5:14166000-14176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:14166400-14177600	Weak transcription	Hela-S3	cervix
4	chr5:14167200-14176000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:14169200-14180400	Enhancers	HepG2	liver
6	chr5:14171400-14176000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:14172000-14178000	Weak transcription	Fetal Brain Female	brain
8	chr5:14172200-14175600	Enhancers	Osteobl	bone
9	chr5:14172200-14176200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:14172600-14178200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:14174200-14177600	Weak transcription	Gastric	stomach
12	chr5:14174400-14176200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:14174400-14177200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:14174400-14178600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:14174400-14183400	Weak transcription	Fetal Lung	lung
16	chr5:14174400-14184400	Weak transcription	Colonic Mucosa	Colon
17	chr5:14174600-14175800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr5:14174600-14177200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:14174600-14177600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:14174600-14177600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:14174600-14177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:14174600-14177600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:14174600-14177600	Weak transcription	Fetal Brain Male	brain
24	chr5:14174600-14177800	Weak transcription	Brain Angular Gyrus	brain
25	chr5:14174600-14177800	Weak transcription	HSMMtube	muscle
26	chr5:14174600-14178200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:14174600-14178400	Enhancers	A549	lung
28	chr5:14174600-14179600	Weak transcription	Fetal Intestine Small	intestine
29	chr5:14174600-14183000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:14174800-14175600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:14174800-14175800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:14174800-14175800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:14174800-14175800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr5:14174800-14175800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:14174800-14176000	Weak transcription	Liver	Liver
36	chr5:14174800-14176200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:14174800-14176200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr5:14174800-14176200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr5:14174800-14176600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:14174800-14176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:14174800-14176600	Weak transcription	Right Atrium	heart
42	chr5:14174800-14176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:14174800-14176800	Enhancers	HUVEC	blood vessel
44	chr5:14174800-14177000	Weak transcription	NHLF	lung
45	chr5:14174800-14177200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:14174800-14177200	Weak transcription	Fetal Heart	heart
47	chr5:14174800-14177200	Weak transcription	Fetal Intestine Large	intestine
48	chr5:14174800-14177200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:14174800-14177200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:14174800-14177400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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