Variant report

Variant	rs36000169
Chromosome Location	chr2:114048018-114048019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10864913	0.83[AMR][1000 genomes]
rs11123176	0.92[AMR][1000 genomes]
rs11123177	0.90[AMR][1000 genomes]
rs11123179	0.90[AMR][1000 genomes]
rs11685107	0.86[AMR][1000 genomes]
rs11685421	0.86[AMR][1000 genomes]
rs11695071	0.83[AMR][1000 genomes]
rs12475140	0.89[AMR][1000 genomes]
rs12476056	0.92[AMR][1000 genomes]
rs2002510	0.89[AMR][1000 genomes]
rs7425070	0.83[AMR][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	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2762785	chr2:114044712-114081784	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs36000169	AC016683.6	cis	lung	GTEx
rs36000169	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs36000169	AC016683.6	cis	Muscle Skeletal	GTEx
rs36000169	AC016683.6	cis	Whole Blood	GTEx
rs36000169	PAX8	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114042600-114048600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:114043200-114048800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:114043600-114048600	Weak transcription	NHEK	skin
4	chr2:114043800-114048600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:114044600-114049200	Enhancers	Fetal Intestine Small	intestine
6	chr2:114044800-114048600	Enhancers	Fetal Intestine Large	intestine
7	chr2:114045400-114049200	Enhancers	Stomach Mucosa	stomach
8	chr2:114046600-114048600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:114046800-114048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:114047000-114048200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:114047000-114048200	Enhancers	HepG2	liver
12	chr2:114047200-114048600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:114048000-114048400	Enhancers	Rectal Mucosa Donor 29	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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