Variant report

Variant	rs12589079
Chromosome Location	chr14:35542493-35542494
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	chr14:35539951..35543515-chr14:35547537..35550740,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151327	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1028449	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11156875	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12050390	0.82[ASN][1000 genomes]
rs12050402	0.84[ASN][1000 genomes]
rs12050404	0.84[ASN][1000 genomes]
rs12050447	0.84[ASN][1000 genomes]
rs12587376	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12880809	0.82[ASN][1000 genomes]
rs12880928	0.86[ASN][1000 genomes]
rs12881698	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12887248	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12887779	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12892552	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12896759	0.88[ASN][1000 genomes]
rs17102967	0.88[ASN][1000 genomes]
rs17102970	0.88[ASN][1000 genomes]
rs17103005	0.84[ASN][1000 genomes]
rs2010648	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2038255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143950	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179890	0.81[ASN][1000 genomes]
rs2273158	0.86[ASN][1000 genomes]
rs2415260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2415261	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2415262	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28365850	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28399702	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34286037	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34737707	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35030792	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs36112862	0.87[ASN][1000 genomes]
rs3809449	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4594164	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5014384	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56686328	0.84[ASN][1000 genomes]
rs57075379	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57725522	0.89[AMR][1000 genomes]
rs58770366	0.81[ASN][1000 genomes]
rs60693825	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61125355	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61136372	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62625038	0.96[ASN][1000 genomes]
rs7141292	0.81[ASN][1000 genomes]
rs71421921	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7142489	0.81[ASN][1000 genomes]
rs7144423	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7144574	0.80[ASN][1000 genomes]
rs7144617	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7145474	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145608	0.84[ASN][1000 genomes]
rs7145883	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7149177	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153068	0.84[ASN][1000 genomes]
rs7153331	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7153550	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7153626	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154306	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155696	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7156322	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7159324	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7160160	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680650	0.81[ASN][1000 genomes]
rs74046408	0.86[ASN][1000 genomes]
rs8006583	0.81[ASN][1000 genomes]
rs8007274	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8009093	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8013540	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8014377	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015622	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8017191	0.86[ASN][1000 genomes]
rs8017225	0.86[ASN][1000 genomes]
rs8018114	0.86[ASN][1000 genomes]
rs941653	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9671773	0.84[ASN][1000 genomes]
rs9672061	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901602	chr14:35367889-35571651	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	nsv901608	chr14:35449467-35571651	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv901609	chr14:35449467-35587767	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv456204	chr14:35466584-35556498	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv564263	chr14:35466584-35556498	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv901612	chr14:35470049-35571651	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv901613	chr14:35470049-35587767	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv901614	chr14:35485748-35571651	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv901615	chr14:35485748-35630175	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
15	nsv1052800	chr14:35509858-35607117	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
17	nsv564265	chr14:35512335-35624831	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
18	nsv1046992	chr14:35527239-35724227	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv1051274	chr14:35529529-35724227	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv1048823	chr14:35537281-35724892	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	nsv542032	chr14:35537281-35724892	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv1040540	chr14:35537481-35724753	Strong transcription Weak transcription Genic enhancers Active TSS 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	27 gene(s)	inside rSNPs	diseases
23	nsv542033	chr14:35537481-35724753	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12589079	KIAA0391	Cis_1M	lymphoblastoid	RTeQTL
rs12589079	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL
rs12589079	PPP2R3C	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35516400-35552600	Weak transcription	Spleen	Spleen
2	chr14:35516800-35551200	Weak transcription	Right Ventricle	heart
3	chr14:35516800-35552200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr14:35517200-35547200	Weak transcription	Brain Anterior Caudate	brain
5	chr14:35517400-35544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:35517400-35578800	Weak transcription	Stomach Mucosa	stomach
7	chr14:35517600-35545800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:35517600-35554400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr14:35518000-35547400	Weak transcription	GM12878-XiMat	blood
10	chr14:35520200-35550800	Weak transcription	NHLF	lung
11	chr14:35521000-35559400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:35526600-35547200	Weak transcription	Brain Angular Gyrus	brain
13	chr14:35526600-35552400	Weak transcription	Brain Substantia Nigra	brain
14	chr14:35528200-35547400	Weak transcription	Fetal Thymus	thymus
15	chr14:35528200-35552200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:35528200-35559400	Weak transcription	Colonic Mucosa	Colon
17	chr14:35528600-35552400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr14:35528600-35552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:35528800-35563200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr14:35529000-35552000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:35529400-35555800	Weak transcription	Aorta	Aorta
22	chr14:35529400-35590200	Weak transcription	Esophagus	oesophagus
23	chr14:35530400-35550600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr14:35530600-35544000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:35530600-35547200	Weak transcription	HMEC	breast
26	chr14:35530600-35548000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:35530600-35550200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr14:35530600-35552400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:35530600-35563600	Weak transcription	Small Intestine	intestine
30	chr14:35530600-35590000	Weak transcription	Fetal Heart	heart
31	chr14:35530800-35552000	Weak transcription	Hela-S3	cervix
32	chr14:35531400-35547400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr14:35531400-35550800	Weak transcription	HUVEC	blood vessel
34	chr14:35531400-35552600	Weak transcription	Pancreas	Pancrea
35	chr14:35531400-35563400	Weak transcription	Gastric	stomach
36	chr14:35531800-35542800	Weak transcription	K562	blood
37	chr14:35531800-35546000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr14:35532800-35544800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr14:35537600-35544400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr14:35537600-35545800	Weak transcription	NHDF-Ad	bronchial
41	chr14:35537800-35543200	Strong transcription	Fetal Intestine Large	intestine
42	chr14:35538200-35542600	Weak transcription	Lung	lung
43	chr14:35538200-35543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:35538200-35545800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:35538200-35546200	Weak transcription	Colon Smooth Muscle	Colon
46	chr14:35538200-35547000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr14:35538200-35547000	Weak transcription	HSMMtube	muscle
48	chr14:35538200-35547400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr14:35538200-35581000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:35538400-35542600	Weak transcription	Stomach Smooth Muscle	stomach

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