Variant report

Variant	rs12090916
Chromosome Location	chr1:166057870-166057871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UCK2-2	chr1:166056324-166059452	NONHSAT007345

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1002160	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10753704	0.89[EUR][1000 genomes]
rs10753709	0.83[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10753710	0.87[EUR][1000 genomes]
rs10800183	0.88[CEU][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs10800184	0.88[EUR][1000 genomes]
rs10800186	0.89[EUR][1000 genomes]
rs10800187	0.90[EUR][1000 genomes]
rs10800191	0.87[EUR][1000 genomes]
rs10800192	0.86[EUR][1000 genomes]
rs10800193	0.87[EUR][1000 genomes]
rs10918344	0.88[EUR][1000 genomes]
rs10918345	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10918347	0.84[EUR][1000 genomes]
rs10918348	0.90[EUR][1000 genomes]
rs10918349	0.90[EUR][1000 genomes]
rs10918362	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10918367	0.87[EUR][1000 genomes]
rs10918368	0.84[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10918370	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10918371	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10918372	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10918373	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10918375	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11487531	0.90[EUR][1000 genomes]
rs11590461	0.90[EUR][1000 genomes]
rs12030010	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12065238	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12078862	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097635	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12123839	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12132672	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12145793	0.85[EUR][1000 genomes]
rs12756802	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs28718625	0.90[EUR][1000 genomes]
rs34402000	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4072242	0.87[EUR][1000 genomes]
rs4147071	0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4147482	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4339838	0.84[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs4542195	0.84[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4657520	0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4657522	0.86[EUR][1000 genomes]
rs55704823	0.90[EUR][1000 genomes]
rs56044172	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59317225	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59384574	0.90[EUR][1000 genomes]
rs6426970	0.87[EUR][1000 genomes]
rs6659245	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6664520	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6692196	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6700318	0.88[EUR][1000 genomes]
rs6700427	0.87[EUR][1000 genomes]
rs72703921	0.88[EUR][1000 genomes]
rs731264	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521995	0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7530896	0.87[EUR][1000 genomes]
rs7553768	0.87[EUR][1000 genomes]
rs919674	0.93[TSI][hapmap];0.87[EUR][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12090916	PVRL4	cis	cerebellum	SCAN
rs12090916	TBX19	cis	parietal	SCAN
rs12090916	CD48	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166049000-166067200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:166051000-166059400	Weak transcription	Right Atrium	heart
3	chr1:166051000-166059600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:166051200-166058800	Weak transcription	Adipose Nuclei	Adipose
5	chr1:166051200-166059200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:166051200-166060000	Weak transcription	Right Ventricle	heart
7	chr1:166051400-166068400	Weak transcription	Pancreas	Pancrea
8	chr1:166051600-166064400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:166051800-166058600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:166053400-166059000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:166053600-166059000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:166054000-166058800	Weak transcription	GM12878-XiMat	blood
13	chr1:166054200-166058600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:166054600-166059000	Weak transcription	Spleen	Spleen
15	chr1:166055000-166059000	Weak transcription	Left Ventricle	heart
16	chr1:166055600-166064600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:166056000-166066200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:166056200-166058600	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:166056200-166058800	Weak transcription	Lung	lung
20	chr1:166056800-166058400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:166057600-166058000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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