Variant report

Variant	rs12652543
Chromosome Location	chr5:14177235-14177236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14176923..14179557-chr5:14181390..14183679,4	MCF-7	breast:
2	chr5:14170146..14172606-chr5:14175990..14178962,3	MCF-7	breast:
3	chr5:14162988..14165248-chr5:14175781..14177322,2	MCF-7	breast:
4	chr5:14175441..14177437-chr5:14177800..14180051,2	MCF-7	breast:
5	chr5:14165692..14168086-chr5:14174628..14177292,2	MCF-7	breast:
6	chr5:14175254..14177607-chr5:14178876..14181098,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs151899	0.91[JPT][hapmap]
rs164109	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs164351	0.83[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs164521	0.81[ASN][1000 genomes]
rs164629	0.86[JPT][hapmap]
rs16903264	0.84[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs26281	0.86[JPT][hapmap]
rs26286	0.82[JPT][hapmap]
rs28014	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs32340	0.84[JPT][hapmap]
rs32549	0.86[JPT][hapmap]
rs32571	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs32573	0.81[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12652543	FBXL7	cis	cerebellum	SCAN
rs12652543	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14164600-14181600	Weak transcription	Esophagus	oesophagus
2	chr5:14166400-14177600	Weak transcription	Hela-S3	cervix
3	chr5:14169200-14180400	Enhancers	HepG2	liver
4	chr5:14172000-14178000	Weak transcription	Fetal Brain Female	brain
5	chr5:14172600-14178200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:14174200-14177600	Weak transcription	Gastric	stomach
7	chr5:14174400-14178600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:14174400-14183400	Weak transcription	Fetal Lung	lung
9	chr5:14174400-14184400	Weak transcription	Colonic Mucosa	Colon
10	chr5:14174600-14177600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:14174600-14177600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:14174600-14177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:14174600-14177600	Weak transcription	Brain Germinal Matrix	brain
14	chr5:14174600-14177600	Weak transcription	Fetal Brain Male	brain
15	chr5:14174600-14177800	Weak transcription	Brain Angular Gyrus	brain
16	chr5:14174600-14177800	Weak transcription	HSMMtube	muscle
17	chr5:14174600-14178200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:14174600-14178400	Enhancers	A549	lung
19	chr5:14174600-14179600	Weak transcription	Fetal Intestine Small	intestine
20	chr5:14174600-14183000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:14174800-14177400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:14174800-14177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:14174800-14177400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:14174800-14177400	Weak transcription	Brain Anterior Caudate	brain
25	chr5:14174800-14177400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:14174800-14177400	Weak transcription	Ovary	ovary
27	chr5:14174800-14177600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:14174800-14177600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:14174800-14177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:14174800-14177600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:14174800-14177600	Weak transcription	Left Ventricle	heart
32	chr5:14174800-14177600	Weak transcription	Lung	lung
33	chr5:14174800-14177600	Weak transcription	Psoas Muscle	Psoas
34	chr5:14174800-14177600	Weak transcription	Right Ventricle	heart
35	chr5:14174800-14177600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:14174800-14177600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:14174800-14177800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:14174800-14177800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:14174800-14177800	Weak transcription	Aorta	Aorta
40	chr5:14174800-14177800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:14174800-14177800	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:14174800-14177800	Weak transcription	Pancreas	Pancrea
43	chr5:14174800-14177800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:14174800-14177800	Weak transcription	Small Intestine	intestine
45	chr5:14174800-14177800	Weak transcription	Spleen	Spleen
46	chr5:14174800-14178000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:14174800-14178200	Weak transcription	Adipose Nuclei	Adipose
48	chr5:14174800-14178400	Weak transcription	Brain Substantia Nigra	brain
49	chr5:14174800-14178400	Weak transcription	HMEC	breast
50	chr5:14174800-14178800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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