Variant report

Variant	rs2153110
Chromosome Location	chr6:145243339-145243340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs1111810	0.81[ASN][1000 genomes]
rs12175408	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12175421	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13195749	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13198108	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13201654	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13210889	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13216871	0.89[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13217690	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1338696	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1338697	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538401	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1538402	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153108	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153109	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2185143	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35285375	0.83[ASN][1000 genomes]
rs35361162	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35946718	0.84[ASN][1000 genomes]
rs4143178	0.91[EUR][1000 genomes]
rs4331996	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4331997	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4526219	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4637659	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4895660	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4896761	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4896762	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57590687	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62438853	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6570657	0.94[EUR][1000 genomes]
rs6570659	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570660	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570661	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570662	0.88[ASN][1000 genomes]
rs6909971	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6910398	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6914560	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6930238	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6931199	0.91[EUR][1000 genomes]
rs6934724	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6935054	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935093	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6935178	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6935436	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7742815	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7742893	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7743204	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7762951	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9283117	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321998	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9321999	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322000	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322001	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322002	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9376873	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376877	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376879	0.81[ASN][1000 genomes]
rs9386088	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9386093	0.81[ASN][1000 genomes]
rs9390249	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9390250	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9399516	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9399517	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9403622	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403624	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403625	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9403626	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9403630	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403636	0.88[ASN][1000 genomes]
rs9497118	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9497128	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9497135	0.85[ASN][1000 genomes]
rs9688347	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9688355	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9688729	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[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
rs2153110	VTA1	cis	cerebellum	SCAN
rs2153110	VTA1	cis	parietal	SCAN
rs2153110	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145234400-145243400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:145240400-145244400	Enhancers	Liver	Liver
3	chr6:145240600-145243600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:145241600-145243400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:145241600-145243400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:145241600-145243800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:145241600-145244200	Enhancers	NHDF-Ad	bronchial
8	chr6:145241800-145243800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:145241800-145243800	Enhancers	Pancreas	Pancrea
10	chr6:145241800-145244200	Enhancers	A549	lung
11	chr6:145242000-145243400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:145242000-145243400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:145242200-145243600	Weak transcription	HSMMtube	muscle
14	chr6:145242400-145243800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:145242400-145243800	Enhancers	HepG2	liver
16	chr6:145242600-145243400	Weak transcription	Gastric	stomach
17	chr6:145242600-145243800	Enhancers	Adipose Nuclei	Adipose
18	chr6:145242600-145243800	Enhancers	Duodenum Mucosa	Duodenum
19	chr6:145242800-145243600	Weak transcription	Stomach Mucosa	stomach
20	chr6:145243000-145243400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:145243200-145243800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
22	chr6:145243200-145243800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:145243200-145244400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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