Variant report

Variant	rs12322087
Chromosome Location	chr12:45592396-45592397
allele	C/T
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	GATA3	chr12:45592056-45592502	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45592116..45593675-chr12:46122728..46125120,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257738	TF binding region
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1025090	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10437984	0.81[EUR][1000 genomes]
rs10459293	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459294	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10459295	1.00[JPT][hapmap]
rs10492284	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10785556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785557	0.81[EUR][1000 genomes]
rs10785569	0.80[JPT][hapmap]
rs10880757	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880758	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880760	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880761	0.87[AMR][1000 genomes]
rs10880762	0.81[EUR][1000 genomes]
rs10880763	0.81[EUR][1000 genomes]
rs10880764	0.81[EUR][1000 genomes]
rs10880765	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs10880766	1.00[JPT][hapmap]
rs10880768	1.00[JPT][hapmap]
rs10880775	0.82[JPT][hapmap]
rs11182898	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182899	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182905	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs11182908	0.91[EUR][1000 genomes]
rs11182912	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11182913	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182916	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182917	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182918	0.81[EUR][1000 genomes]
rs11182919	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182921	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182922	0.81[EUR][1000 genomes]
rs11182923	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182927	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182931	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182935	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182936	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182938	0.81[EUR][1000 genomes]
rs11182939	0.81[EUR][1000 genomes]
rs11182940	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182941	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182942	0.87[ASN][1000 genomes]
rs11182943	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182944	0.81[EUR][1000 genomes]
rs11182946	0.81[EUR][1000 genomes]
rs11182947	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182953	0.82[ASN][1000 genomes]
rs11182954	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11182955	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11182957	1.00[JPT][hapmap]
rs11182961	1.00[JPT][hapmap]
rs11182965	1.00[JPT][hapmap]
rs11182981	1.00[JPT][hapmap]
rs11182983	0.82[JPT][hapmap]
rs11182986	0.80[JPT][hapmap]
rs11182988	0.80[JPT][hapmap]
rs11182989	0.82[JPT][hapmap]
rs11182990	0.82[JPT][hapmap]
rs11561532	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11610233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612203	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11612233	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11614082	1.00[JPT][hapmap]
rs11614089	0.94[JPT][hapmap]
rs11615850	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12226944	0.91[ASN][1000 genomes]
rs12227678	0.89[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12228733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230322	0.81[EUR][1000 genomes]
rs12231753	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs12299174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320168	0.81[EUR][1000 genomes]
rs12320437	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12814332	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12815115	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12815334	0.82[ASN][1000 genomes]
rs12815723	0.82[ASN][1000 genomes]
rs12822746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12828052	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13378014	0.82[JPT][hapmap]
rs17095551	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17095557	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2052602	0.81[EUR][1000 genomes]
rs2408184	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2408185	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34024171	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35054776	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35588430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35660715	0.81[EUR][1000 genomes]
rs3759077	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759080	0.81[EUR][1000 genomes]
rs3759081	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759082	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782131	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57560057	0.82[ASN][1000 genomes]
rs57797434	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923804	0.86[EUR][1000 genomes]
rs61923810	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923825	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923830	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7138983	0.90[AMR][1000 genomes]
rs7954282	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7963038	0.81[EUR][1000 genomes]
rs7963057	0.81[EUR][1000 genomes]
rs9739519	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12322087	TMEM16F	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45570000-45593200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:45571000-45594600	Weak transcription	Pancreas	Pancrea
3	chr12:45573400-45594600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:45573600-45593600	Weak transcription	Fetal Thymus	thymus
5	chr12:45578600-45594000	Weak transcription	Thymus	Thymus
6	chr12:45578600-45594600	Weak transcription	Psoas Muscle	Psoas
7	chr12:45579400-45599200	Weak transcription	Primary B cells from cord blood	blood
8	chr12:45580200-45593800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:45582400-45593600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:45584800-45594400	Weak transcription	Aorta	Aorta
11	chr12:45585200-45593800	Weak transcription	Small Intestine	intestine
12	chr12:45586600-45594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:45586600-45602400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:45586800-45593800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:45587000-45593000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:45587200-45594600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:45587400-45593000	Weak transcription	Fetal Intestine Large	intestine
18	chr12:45587400-45593000	Weak transcription	Dnd41	blood
19	chr12:45587400-45593600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:45587800-45593000	Weak transcription	HepG2	liver
21	chr12:45588400-45593800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:45592200-45592400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:45592200-45593000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr12:45592200-45593200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:45592200-45599400	Enhancers	Primary monocytes fromperipheralblood	blood

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