Variant report

Variant	rs1338697
Chromosome Location	chr6:145215653-145215654
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	chr6:145199307..145201397-chr6:145215115..145217715,2	MCF-7	breast:
2	chr6:145215634..145217242-chr6:145456840..145459220,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs12175408	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12175421	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13195749	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13198108	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13201654	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13210889	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13216871	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13217690	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1338696	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538401	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1538402	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2153108	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2153109	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2153110	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2185143	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35285375	0.92[ASN][1000 genomes]
rs35361162	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35946718	0.93[ASN][1000 genomes]
rs4143178	0.92[EUR][1000 genomes]
rs4331996	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4331997	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4526219	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4637659	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4895660	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4896761	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4896762	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57590687	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62438853	0.89[EUR][1000 genomes]
rs6570657	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6570659	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570660	0.82[EUR][1000 genomes]
rs6570661	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6909971	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910398	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914560	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930238	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6931199	0.92[EUR][1000 genomes]
rs6934724	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935054	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935093	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935178	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935436	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7742815	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7742893	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7743204	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7762951	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9283117	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9285505	0.82[ASN][1000 genomes]
rs9321998	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9321999	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9322000	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322001	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322002	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322003	0.82[ASN][1000 genomes]
rs9322004	0.82[ASN][1000 genomes]
rs9376873	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376877	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9386088	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390249	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390250	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399516	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399517	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9403622	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9403624	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403625	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403626	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403627	0.82[ASN][1000 genomes]
rs9403630	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9497118	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9497120	0.85[ASN][1000 genomes]
rs9497121	0.85[ASN][1000 genomes]
rs9497128	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9688347	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9688355	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9688729	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv1850377	chr6:145199259-145319640	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1338697	VTA1	cis	cerebellum	SCAN
rs1338697	PLAGL1	cis	cerebellum	SCAN
rs1338697	VTA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145210600-145217000	Weak transcription	Right Atrium	heart
2	chr6:145214400-145216400	Enhancers	A549	lung
3	chr6:145214800-145218400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:145215200-145215800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:145215200-145215800	Enhancers	Fetal Intestine Small	intestine
6	chr6:145215200-145216000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:145215400-145216000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:145215400-145218000	Weak transcription	HSMMtube	muscle
9	chr6:145215400-145220800	Enhancers	Osteobl	bone
10	chr6:145215600-145215800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:145215600-145215800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:145215600-145215800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:145215600-145216000	Enhancers	Fetal Thymus	thymus

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