Variant report

Variant	rs11900469
Chromosome Location	chr2:128193698-128193699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10201047	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10928765	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10928766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679431	0.87[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs11680815	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12618494	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12619972	0.92[EUR][1000 genomes]
rs12623334	0.90[EUR][1000 genomes]
rs13011041	0.90[EUR][1000 genomes]
rs13389029	0.89[EUR][1000 genomes]
rs1568277	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1568279	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17015274	0.89[EUR][1000 genomes]
rs334135	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs3889307	0.87[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs4374323	0.81[ASN][1000 genomes]
rs4662732	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs56106399	0.89[EUR][1000 genomes]
rs58880408	0.89[EUR][1000 genomes]
rs62160265	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62160266	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62160287	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62160288	0.98[EUR][1000 genomes]
rs62160289	0.92[EUR][1000 genomes]
rs62160291	0.90[EUR][1000 genomes]
rs66609069	0.96[EUR][1000 genomes]
rs6716489	0.89[EUR][1000 genomes]
rs67495946	0.98[EUR][1000 genomes]
rs7586672	0.82[CEU][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs880933	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11900469	AC068282.3	cis	Thyroid	GTEx
rs11900469	AC068282.3	cis	Esophagus Mucosa	GTEx
rs11900469	AC068282.3	cis	Nerve Tibial	GTEx
rs11900469	AC068282.3	cis	Esophagus Muscularis	GTEx
rs11900469	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11900469	AC068282.3	cis	Artery Tibial	GTEx
rs11900469	AC068282.3	cis	lung	GTEx
rs11900469	MAP3K2	cis	multi-tissue	Pritchard
rs11900469	AC068282.3	cis	Whole Blood	GTEx
rs11900469	AC068282.3	cis	Heart Left Ventricle	GTEx
rs11900469	AC068282.3	cis	Stomach	GTEx
rs11900469	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs11900469	AC068282.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128181400-128194000	Weak transcription	Gastric	stomach
2	chr2:128181400-128195200	Weak transcription	Pancreas	Pancrea
3	chr2:128181400-128196000	Weak transcription	Lung	lung
4	chr2:128181400-128209800	Weak transcription	Right Atrium	heart
5	chr2:128181600-128195000	Weak transcription	Fetal Intestine Large	intestine
6	chr2:128181600-128197200	Weak transcription	Brain Anterior Caudate	brain
7	chr2:128183000-128197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:128184800-128195200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:128186400-128195000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:128186400-128195600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:128189400-128195200	Weak transcription	Fetal Intestine Small	intestine
12	chr2:128190200-128194000	Weak transcription	Liver	Liver
13	chr2:128190200-128195600	Weak transcription	A549	lung
14	chr2:128193600-128195400	Enhancers	HepG2	liver

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