Variant report

Variant	rs1639065
Chromosome Location	chr7:2893339-2893340
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	chr7:2882956..2885508-chr7:2891694..2894640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1182156	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13230946	0.87[ASN][1000 genomes]
rs1614791	0.81[ASN][1000 genomes]
rs1623138	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1636248	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1636251	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1636252	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1636255	0.81[ASN][1000 genomes]
rs1636256	0.88[ASN][1000 genomes]
rs1639034	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1639064	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1639066	0.81[ASN][1000 genomes]
rs1713912	0.83[ASN][1000 genomes]
rs1713913	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1713921	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2527680	0.81[ASN][1000 genomes]
rs2527681	0.81[ASN][1000 genomes]
rs2533875	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2533889	0.81[ASN][1000 genomes]
rs2533891	0.81[ASN][1000 genomes]
rs2644293	0.81[ASN][1000 genomes]
rs2644309	0.81[ASN][1000 genomes]
rs2679259	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7783400	0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1639065	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1639065	GNA12	cis	Nerve Tibial	GTEx
rs1639065	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 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	chr7:2891400-2893400	Enhancers	GM12878-XiMat	blood
8	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:2891600-2902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:2891600-2902800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr7:2892000-2893400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:2892400-2893400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:2892400-2893400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr7:2892400-2893400	Enhancers	NHDF-Ad	bronchial
16	chr7:2892400-2893400	Enhancers	Osteobl	bone
17	chr7:2892800-2893400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:2892800-2902000	Weak transcription	NHLF	lung
19	chr7:2893000-2893400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr7:2893200-2895800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:2893200-2902000	Weak transcription	Ovary	ovary

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