Variant report

Variant	rs2527680
Chromosome Location	chr7:2892361-2892362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2890202..2892822-chr7:2894073..2897035,2	MCF-7	breast:
2	chr7:2891216..2892935-chr7:2895055..2897737,2	K562	blood:
3	chr7:2882956..2885508-chr7:2891694..2894640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1182155	0.84[EUR][1000 genomes]
rs1182174	0.83[EUR][1000 genomes]
rs1182176	0.82[EUR][1000 genomes]
rs1182177	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1182178	0.82[EUR][1000 genomes]
rs1182179	0.82[EUR][1000 genomes]
rs1182181	0.82[EUR][1000 genomes]
rs1182182	0.82[EUR][1000 genomes]
rs1182183	0.82[EUR][1000 genomes]
rs1182184	0.82[EUR][1000 genomes]
rs1182185	0.81[EUR][1000 genomes]
rs1182186	0.81[EUR][1000 genomes]
rs1182198	0.81[EUR][1000 genomes]
rs1183085	0.82[EUR][1000 genomes]
rs11973498	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12700373	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13230946	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13230995	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1614791	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636247	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1636248	0.89[ASN][1000 genomes]
rs1636249	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636250	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636251	0.92[ASN][1000 genomes]
rs1636252	0.94[ASN][1000 genomes]
rs1636253	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636254	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636256	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1639034	0.94[ASN][1000 genomes]
rs1639036	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1639040	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1639065	0.81[ASN][1000 genomes]
rs1639066	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713912	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1713921	0.90[ASN][1000 genomes]
rs2107964	0.81[EUR][1000 genomes]
rs2527677	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527681	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533867	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533868	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533870	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2533871	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2533875	0.90[ASN][1000 genomes]
rs2533877	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533878	0.85[EUR][1000 genomes]
rs2533889	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533891	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644281	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644286	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644293	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644300	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2644309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679259	0.94[ASN][1000 genomes]
rs71522301	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71522302	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71524003	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7783400	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3398295	chr7:2887626-2892424	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2527680	GNA12	cis	multi-tissue	Pritchard
rs2527680	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2527680	GNA12	cis	Artery Tibial	GTEx
rs2527680	GNA12	cis	Nerve Tibial	GTEx

Chromatin state (count:22 , 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	chr7:2891000-2892400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:2891200-2892400	Weak transcription	NHDF-Ad	bronchial
9	chr7:2891200-2892800	Weak transcription	NH-A	brain
10	chr7:2891400-2892400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:2891400-2892400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:2891400-2892400	Weak transcription	Osteobl	bone
13	chr7:2891400-2893000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr7:2891400-2893400	Enhancers	GM12878-XiMat	blood
15	chr7:2891600-2892800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:2891600-2902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:2891600-2902800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:2892000-2893400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:2892200-2893200	Enhancers	Adipose Nuclei	Adipose
22	chr7:2892200-2893200	Enhancers	Skeletal Muscle Male	skeletal muscle

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