Variant report

Variant	rs12185025
Chromosome Location	chr14:82003076-82003077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr14:82002777-82003216	MCF-7	breast:	n/a	n/a
2	FOXA1	chr14:82002716-82003154	T-47D	breast:	n/a	chr14:82002883-82002898 chr14:82002858-82002870
3	FOXA1	chr14:82002684-82003143	T-47D	breast:	n/a	chr14:82002883-82002898 chr14:82002858-82002870
4	ESR1	chr14:82002727-82003168	T-47D	breast:	n/a	n/a
5	JUND	chr14:82002648-82003383	T-47D	breast:	n/a	n/a
6	GATA3	chr14:82002709-82003186	T-47D	breast:	n/a	chr14:82002716-82002725
7	GATA3	chr14:82002597-82003292	MCF-7	breast:	n/a	chr14:82002716-82002725 chr14:82003211-82003221
8	GATA3	chr14:82002658-82003320	T-47D	breast:	n/a	chr14:82002716-82002725 chr14:82003211-82003221
9	ESR1	chr14:82002710-82003136	T-47D	breast:	n/a	n/a
10	NR2F2	chr14:82002638-82003295	MCF-7	breast:	n/a	n/a
11	EP300	chr14:82002690-82003212	T-47D	breast:	n/a	chr14:82002969-82002979
12	TCF7L2	chr14:82002957-82003881	MCF-7	breast:	n/a	chr14:82003537-82003551 chr14:82003540-82003549 chr14:82003678-82003687 chr14:82003675-82003689 chr14:82003676-82003690
13	NR2F2	chr14:82002643-82003233	MCF-7	breast:	n/a	n/a
14	GATA3	chr14:82002651-82003297	MCF-7	breast:	n/a	chr14:82002716-82002725 chr14:82003211-82003221
15	EP300	chr14:82002680-82003292	T-47D	breast:	n/a	chr14:82002969-82002979

Variant related genes	Relation type
SEL1L	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11159500	1.00[YRI][hapmap]
rs12100962	1.00[YRI][hapmap]
rs12100967	1.00[YRI][hapmap]
rs12101219	1.00[YRI][hapmap]
rs12434541	0.86[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12435998	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12436488	0.93[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12586522	1.00[YRI][hapmap]
rs12586817	1.00[YRI][hapmap]
rs12589111	1.00[YRI][hapmap]
rs17111805	1.00[YRI][hapmap]
rs17111807	1.00[YRI][hapmap]
rs17111817	1.00[YRI][hapmap]
rs17111825	1.00[YRI][hapmap]
rs17560087	0.86[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998386	1.00[YRI][hapmap]
rs2371601	1.00[YRI][hapmap]
rs3853422	1.00[YRI][hapmap]
rs56357710	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57665733	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61986625	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61986626	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61986627	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61988565	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691458	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs731390	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047694	chr14:81831147-82534026	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv542145	chr14:81831147-82534026	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
3	nsv902120	chr14:81953242-82067555	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv565299	chr14:81983027-82586324	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1803387	chr14:81995306-82009830	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1803430	chr14:81995306-82009830	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12185025	GSTZ1	cis	parietal	SCAN
rs12185025	ADCK1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:82001000-82003200	Enhancers	Fetal Intestine Small	intestine
2	chr14:82001200-82003800	Enhancers	Fetal Intestine Large	intestine
3	chr14:82001200-82004200	Enhancers	Liver	Liver
4	chr14:82001400-82004200	Enhancers	HepG2	liver
5	chr14:82001800-82003600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr14:82002000-82004400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr14:82002200-82004800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:82002200-82007600	Weak transcription	Pancreas	Pancrea
9	chr14:82002400-82003800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:82002400-82004200	Enhancers	NHEK	skin
11	chr14:82002600-82003200	Enhancers	GM12878-XiMat	blood
12	chr14:82002600-82003600	Weak transcription	Aorta	Aorta
13	chr14:82002600-82004200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr14:82002800-82003200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr14:82002800-82004000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:82003000-82003200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr14:82003000-82003200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr14:82003000-82003200	Enhancers	Gastric	stomach
19	chr14:82003000-82003200	Enhancers	Ovary	ovary
20	chr14:82003000-82003400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr14:82003000-82003800	Enhancers	HMEC	breast

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