Variant report

Variant	rs2929320
Chromosome Location	chr7:124702667-124702668
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	chr7:124701246..124703610-chr7:124820642..124822320,2	MCF-7	breast:

Extended variants
information (count: 179 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:176)

rs_ID	r²[population]
rs10081226	0.84[ASN][1000 genomes]
rs10081265	0.84[ASN][1000 genomes]
rs10081290	0.82[ASN][1000 genomes]
rs10081336	0.84[ASN][1000 genomes]
rs10081375	0.84[ASN][1000 genomes]
rs1011721	0.85[ASN][1000 genomes]
rs1011722	0.85[ASN][1000 genomes]
rs1011723	0.85[ASN][1000 genomes]
rs1021080	0.92[ASN][1000 genomes]
rs10227119	0.83[ASN][1000 genomes]
rs10228459	0.82[ASN][1000 genomes]
rs10231355	0.84[ASN][1000 genomes]
rs10231491	0.81[ASN][1000 genomes]
rs10231818	0.84[ASN][1000 genomes]
rs10239507	0.85[ASN][1000 genomes]
rs10243479	0.81[ASN][1000 genomes]
rs10243992	0.84[ASN][1000 genomes]
rs10252072	0.82[ASN][1000 genomes]
rs10252579	0.92[ASN][1000 genomes]
rs10252798	0.92[ASN][1000 genomes]
rs10255638	0.84[ASN][1000 genomes]
rs10257712	0.84[ASN][1000 genomes]
rs10264288	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10264766	0.84[ASN][1000 genomes]
rs1026837	0.93[ASN][1000 genomes]
rs1026839	0.93[ASN][1000 genomes]
rs10272889	0.84[ASN][1000 genomes]
rs10274820	0.92[ASN][1000 genomes]
rs10279816	0.84[ASN][1000 genomes]
rs10280341	0.84[ASN][1000 genomes]
rs1031955	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10500098	0.93[ASN][1000 genomes]
rs10954050	0.84[ASN][1000 genomes]
rs10954051	0.84[ASN][1000 genomes]
rs10954056	0.84[ASN][1000 genomes]
rs10954062	0.92[ASN][1000 genomes]
rs11763920	0.93[ASN][1000 genomes]
rs11767649	0.92[ASN][1000 genomes]
rs11767737	0.92[ASN][1000 genomes]
rs11769711	0.84[ASN][1000 genomes]
rs11975363	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981797	0.84[ASN][1000 genomes]
rs12111658	0.84[ASN][1000 genomes]
rs12111660	0.84[ASN][1000 genomes]
rs12112909	0.84[ASN][1000 genomes]
rs12534466	0.93[ASN][1000 genomes]
rs12536146	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12538641	0.85[ASN][1000 genomes]
rs12706629	0.84[ASN][1000 genomes]
rs13231916	0.93[ASN][1000 genomes]
rs13240043	0.91[ASN][1000 genomes]
rs13240512	0.84[ASN][1000 genomes]
rs13307657	0.85[ASN][1000 genomes]
rs1351471	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1383749	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383750	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383751	0.84[ASN][1000 genomes]
rs1481328	0.92[ASN][1000 genomes]
rs1481329	0.92[ASN][1000 genomes]
rs1481331	0.84[ASN][1000 genomes]
rs1481332	0.84[ASN][1000 genomes]
rs1481337	0.93[ASN][1000 genomes]
rs1481338	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481339	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1481340	0.84[ASN][1000 genomes]
rs1481343	0.93[ASN][1000 genomes]
rs1531715	0.92[ASN][1000 genomes]
rs1531716	0.92[ASN][1000 genomes]
rs1552119	0.92[ASN][1000 genomes]
rs1552120	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1600738	0.93[ASN][1000 genomes]
rs1600739	0.93[ASN][1000 genomes]
rs1600740	0.93[ASN][1000 genomes]
rs1600743	0.84[ASN][1000 genomes]
rs1600745	0.84[ASN][1000 genomes]
rs1600746	0.84[ASN][1000 genomes]
rs1842615	0.83[ASN][1000 genomes]
rs1842616	0.84[ASN][1000 genomes]
rs1871770	0.92[ASN][1000 genomes]
rs1994022	0.84[ASN][1000 genomes]
rs1994023	0.84[ASN][1000 genomes]
rs2017928	0.92[ASN][1000 genomes]
rs2127971	0.85[ASN][1000 genomes]
rs2170353	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2219953	0.93[ASN][1000 genomes]
rs2402756	0.84[ASN][1000 genomes]
rs2402760	0.84[ASN][1000 genomes]
rs2402762	0.85[ASN][1000 genomes]
rs2402763	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28491035	0.90[ASN][1000 genomes]
rs28807101	0.85[ASN][1000 genomes]
rs28817916	0.84[ASN][1000 genomes]
rs28820311	0.84[ASN][1000 genomes]
rs2929323	1.00[ASN][1000 genomes]
rs2949802	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968867	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34630567	0.92[ASN][1000 genomes]
rs34865746	0.93[ASN][1000 genomes]
rs35929436	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3900363	0.93[ASN][1000 genomes]
rs3903521	0.93[ASN][1000 genomes]
rs3903522	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3903523	0.93[ASN][1000 genomes]
rs4272297	0.93[ASN][1000 genomes]
rs4461840	0.82[ASN][1000 genomes]
rs585608	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs589823	0.92[ASN][1000 genomes]
rs597279	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs606229	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs607260	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs616697	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs635682	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs635736	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs636161	0.92[ASN][1000 genomes]
rs636721	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs637482	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639239	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6466963	0.83[ASN][1000 genomes]
rs6466964	0.84[ASN][1000 genomes]
rs6466965	0.84[ASN][1000 genomes]
rs6466966	0.84[ASN][1000 genomes]
rs6466967	0.84[ASN][1000 genomes]
rs6466968	0.84[ASN][1000 genomes]
rs6466969	0.84[ASN][1000 genomes]
rs6466970	0.85[ASN][1000 genomes]
rs6466971	0.84[ASN][1000 genomes]
rs6466972	0.85[ASN][1000 genomes]
rs6466982	0.93[ASN][1000 genomes]
rs6466990	0.94[ASN][1000 genomes]
rs6466993	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651869	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs659987	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662165	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs665753	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs672965	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676037	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683707	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684345	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs685909	0.92[ASN][1000 genomes]
rs6945951	0.93[ASN][1000 genomes]
rs6954614	0.92[ASN][1000 genomes]
rs6964090	0.93[ASN][1000 genomes]
rs6971179	0.82[ASN][1000 genomes]
rs6971413	0.85[ASN][1000 genomes]
rs719972	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7776744	0.83[ASN][1000 genomes]
rs7776821	0.93[ASN][1000 genomes]
rs7777126	0.85[ASN][1000 genomes]
rs7778956	0.84[AFR][1000 genomes]
rs7779594	0.92[ASN][1000 genomes]
rs7780392	0.84[ASN][1000 genomes]
rs7786384	0.84[ASN][1000 genomes]
rs7787025	0.85[ASN][1000 genomes]
rs7787765	0.85[ASN][1000 genomes]
rs7788066	0.91[ASN][1000 genomes]
rs7788458	0.92[ASN][1000 genomes]
rs7790975	0.84[ASN][1000 genomes]
rs7791399	0.84[ASN][1000 genomes]
rs7791488	0.84[ASN][1000 genomes]
rs7795199	0.84[ASN][1000 genomes]
rs7795218	0.84[ASN][1000 genomes]
rs7795233	0.84[ASN][1000 genomes]
rs7795605	0.84[ASN][1000 genomes]
rs7795611	0.84[ASN][1000 genomes]
rs7795934	0.92[ASN][1000 genomes]
rs7799518	0.84[ASN][1000 genomes]
rs7799523	0.84[ASN][1000 genomes]
rs7799535	0.84[ASN][1000 genomes]
rs7802007	0.92[ASN][1000 genomes]
rs7802210	0.92[ASN][1000 genomes]
rs7806126	0.85[ASN][1000 genomes]
rs7806548	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900047	0.92[ASN][1000 genomes]
rs9332427	0.84[ASN][1000 genomes]
rs9691875	0.92[ASN][1000 genomes]
rs9692367	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv889139	chr7:124600505-124767295	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2929320	RP11-3B12.4	cis	Artery Tibial	GTEx
rs2929320	RP11-3B12.1	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124699800-124702800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:124699800-124703400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr7:124700600-124702800	Enhancers	HUVEC	blood vessel
4	chr7:124700600-124703600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:124701000-124702800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:124701000-124703000	Enhancers	Hela-S3	cervix
7	chr7:124701200-124703400	Weak transcription	Brain Substantia Nigra	brain
8	chr7:124701600-124703000	Weak transcription	Brain Anterior Caudate	brain
9	chr7:124702200-124703200	Weak transcription	Brain Angular Gyrus	brain
10	chr7:124702200-124703200	Weak transcription	NH-A	brain
11	chr7:124702200-124706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:124702200-124712200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:124702400-124703000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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