Variant report

Variant	rs2102294
Chromosome Location	chr12:116991459-116991460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:116990998..116993125-chr14:35021867..35023994,2	MCF-7	breast:
2	chr12:116990108..116992302-chr12:116995187..116997427,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171471	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10774871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10774872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10850662	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10850663	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068062	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068070	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068075	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11609040	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11609872	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11610226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11615960	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394801	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394802	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2047952	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089222	0.94[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs2893685	0.90[ASN][1000 genomes]
rs60521218	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6490075	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6490076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297552	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300418	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7304300	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315385	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954181	0.87[ASN][1000 genomes]
rs7961538	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7969190	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7969566	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972701	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976256	0.92[EUR][1000 genomes];0.93[ASN][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	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2102294	FLJ42957	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116984200-116996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:116984200-116997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:116986600-116993000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:116986600-116993400	Weak transcription	Fetal Brain Male	brain
5	chr12:116986600-116994800	Weak transcription	Thymus	Thymus
6	chr12:116987600-116994400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:116988800-116992800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:116989200-116991600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr12:116989400-116991600	Enhancers	K562	blood
10	chr12:116990200-116994800	Weak transcription	NH-A	brain
11	chr12:116990400-116991600	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:116990400-116994600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:116990400-116994800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:116990400-116995200	Weak transcription	NHEK	skin
15	chr12:116990600-116995200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:116990600-116995200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:116990800-116995200	Weak transcription	Spleen	Spleen
18	chr12:116990800-116996400	Weak transcription	Placenta	Placenta
19	chr12:116990800-116996800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:116991000-116994400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:116991200-116991600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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