Variant report

Variant	rs1639066
Chromosome Location	chr7:2892972-2892973
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	chr7:2882956..2885508-chr7:2891694..2894640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1182155	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1182174	0.80[CEU][hapmap]
rs11973498	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12700373	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13230946	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13230995	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1614791	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636247	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1636248	0.89[ASN][1000 genomes]
rs1636249	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636250	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636251	0.92[ASN][1000 genomes]
rs1636252	0.94[ASN][1000 genomes]
rs1636253	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636254	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636255	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636256	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1639034	0.94[ASN][1000 genomes]
rs1639036	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1639040	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1639065	0.81[ASN][1000 genomes]
rs1713912	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1713921	0.90[ASN][1000 genomes]
rs2107964	0.82[CEU][hapmap]
rs2527677	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527680	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527681	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533867	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533868	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533870	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533871	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2533875	0.90[ASN][1000 genomes]
rs2533877	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533889	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533891	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644281	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644286	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644293	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644300	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2644309	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679259	0.94[ASN][1000 genomes]
rs71522301	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71522302	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71524003	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7783400	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	28 gene(s)	inside rSNPs	diseases
3	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1639066	GNA12	cis	Artery Tibial	GTEx
rs1639066	GNA12	cis	multi-tissue	Pritchard
rs1639066	GNA12	cis	Nerve Tibial	GTEx
rs1639066	GNA12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2884600-2896000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:2884600-2902800	Weak transcription	Right Ventricle	heart
3	chr7:2884800-2895800	Weak transcription	Fetal Heart	heart
4	chr7:2885000-2902000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:2890400-2895800	Weak transcription	Pancreas	Pancrea
6	chr7:2890400-2896400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:2891400-2893000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:2891400-2893400	Enhancers	GM12878-XiMat	blood
9	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:2891600-2902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:2891600-2902800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:2892000-2893400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:2892200-2893200	Enhancers	Adipose Nuclei	Adipose
15	chr7:2892200-2893200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr7:2892400-2893200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:2892400-2893200	Enhancers	Ovary	ovary
18	chr7:2892400-2893400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:2892400-2893400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr7:2892400-2893400	Enhancers	NHDF-Ad	bronchial
21	chr7:2892400-2893400	Enhancers	Osteobl	bone
22	chr7:2892800-2893200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:2892800-2893200	Enhancers	NH-A	brain
24	chr7:2892800-2893400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:2892800-2902000	Weak transcription	NHLF	lung

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