Variant report

Variant	rs12589576
Chromosome Location	chr14:34988067-34988068
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:34987498..34989819-chr14:35007397..35008989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129518	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12050290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12434523	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12435717	0.91[ASW][hapmap];0.95[CEU][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs12588228	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588878	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878854	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12882703	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12894795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12895640	0.95[CEU][hapmap]
rs13826	0.91[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs17524152	0.91[ASW][hapmap];0.95[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs34356189	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34437689	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35091031	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4368076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4592561	0.94[EUR][1000 genomes]
rs55858014	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56801633	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61979674	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61981527	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61981529	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650487	0.95[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7146042	0.95[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs7158829	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040980	chr14:34345018-35255592	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1051104	chr14:34592378-35007083	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv949738	chr14:34616331-34990688	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv564192	chr14:34725233-34996507	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv564193	chr14:34728127-35000188	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv528989	chr14:34744426-34998705	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1054949	chr14:34834260-34992049	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv542025	chr14:34834260-34992049	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv901600	chr14:34895977-35010041	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1037857	chr14:34943388-35007724	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv542026	chr14:34943388-35007724	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1048408	chr14:34958352-35255592	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	nsv1049048	chr14:34969406-35048672	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
14	nsv1042294	chr14:34974774-35017859	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv1053274	chr14:34980184-35020973	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1037503	chr14:34980184-35027115	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
17	nsv564194	chr14:34985645-35029396	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12589576	EAPP	cis	cerebellum	SCAN
rs12589576	EAPP	cis	parietal	SCAN
rs12589576	FAM177A1	cis	cerebellum	SCAN
rs12589576	AKAP6	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:34972200-34989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:34975600-34988200	Weak transcription	Gastric	stomach
3	chr14:34975600-34989800	Weak transcription	Pancreas	Pancrea
4	chr14:34979600-34989600	Weak transcription	Psoas Muscle	Psoas
5	chr14:34980000-34990200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr14:34980600-34991200	Weak transcription	Fetal Kidney	kidney
7	chr14:34980600-34993800	Weak transcription	K562	blood
8	chr14:34981400-34992600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:34982000-34989600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr14:34982600-34991600	Weak transcription	HSMM	muscle
11	chr14:34983200-34988200	Weak transcription	Right Ventricle	heart
12	chr14:34983200-34991800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:34983200-34991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:34983600-34989800	Weak transcription	Hela-S3	cervix
15	chr14:34983800-34990400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr14:34983800-34991600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:34984400-34988200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr14:34984400-34989600	Strong transcription	Fetal Intestine Small	intestine
19	chr14:34984400-35006600	Strong transcription	Fetal Muscle Leg	muscle
20	chr14:34984600-35005800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr14:34984800-34989400	Strong transcription	Fetal Intestine Large	intestine
22	chr14:34984800-34998200	Strong transcription	Brain Germinal Matrix	brain
23	chr14:34984800-35002600	Strong transcription	Ovary	ovary
24	chr14:34984800-35003800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr14:34984800-35004400	Strong transcription	Adipose Nuclei	Adipose
26	chr14:34984800-35005800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:34984800-35006600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr14:34984800-35006800	Strong transcription	Fetal Stomach	stomach
29	chr14:34985000-34989000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:34985000-34989800	Strong transcription	HepG2	liver
31	chr14:34985000-35003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:34985000-35003800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr14:34985000-35004000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr14:34985000-35004800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr14:34985000-35005400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr14:34985000-35005600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr14:34985000-35005800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr14:34985000-35005800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr14:34985000-35005800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr14:34985000-35006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:34985000-35006800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:34985200-34988600	Strong transcription	Fetal Brain Female	brain
43	chr14:34985200-35003600	Strong transcription	Brain Cingulate Gyrus	brain
44	chr14:34985200-35005400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr14:34985200-35005600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr14:34985200-35005600	Strong transcription	Liver	Liver
47	chr14:34985200-35005800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr14:34985200-35006600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr14:34985200-35007000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr14:34985400-34989000	Strong transcription	Primary B cells from cord blood	blood

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